reports/preprocessing_log.txt Version 1
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_tr2/_A_01_assembly2-rnaSPAdes/
SEEK ID: https://fairdomhub.org/data_files/5941?version=1
Filename:
reports/preprocessing_log.txt
Format: Plain text document
Size: 173 KB
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbduk.sh -Xmx230g in=./input/SUSPHIRE_1.fastq in2=./input/SUSPHIRE_2.fastq out=./input/SUSPHIRE_trimmed.fastq ktrim=r k=23 mink=11 hdist=1 ref=/DATA/m arkop/bbmap/resources/adapters.fa tbo tpe maxns=0 trimq=20 qtrim=r maq=12
java -ea -Xmx230g -Xms230g -cp /DATA/markop/bbmap/current/ jgi.BBDuk -Xmx230g in=./input/SUSPHIRE_1.fastq in2=./input/SUSPHIRE_2.fastq out=./input/SUSPHIRE_trimmed.fastq ktrim=r k=23 mink=11 hdist=1 ref=/DATA/markop/bbmap/resour ces/adapters.fa tbo tpe maxns=0 trimq=20 qtrim=r maq=12
Executing jgi.BBDuk [-Xmx230g, in=./input/SUSPHIRE_1.fastq, in2=./input/SUSPHIRE_2.fastq, out=./input/SUSPHIRE_trimmed.fastq, ktrim=r, k=23, mink=11, hdist=1, ref=/DATA/markop/bbmap/resources/adapters.fa, tbo, tpe, maxns=0, trim q=20, qtrim=r, maq=12]
Version 38.34
maskMiddle was disabled because useShortKmers=true
0.042 seconds.
Initial:
Memory: max=236670m, total=236670m, free=228027m, used=8643m
Added 217045 kmers; time: 0.169 seconds.
Memory: max=236670m, total=236670m, free=216913m, used=19757m
Input is being processed as paired
Started output streams: 0.034 seconds.
Processing time: 5235.308 seconds.
Input: 695202748 reads 104280412200 bases.
QTrimmed: 123759759 reads (17.80%) 4453364269 bases (4.27%)
KTrimmed: 109170582 reads (15.70%) 3716369054 bases (3.56%)
Trimmed by overlap: 32875586 reads (4.73%) 193234434 bases (0.19%)
Low quality discards: 30062466 reads (4.32%) 4005006752 bases (3.84%)
Total Removed: 31815186 reads (4.58%) 12367974509 bases (11.86%)
Result: 663387562 reads (95.42%) 91912437691 bases (88.14%)
Time: 5235.518 seconds.
Reads Processed: 695m 132.79k reads/sec
Bases Processed: 104280m 19.92m bases/sec
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbduk.sh -Xmx230g in=./input/Edinburgh50_1.fastq in2=./input/Edinburgh50_2.fastq out=./input/Edinburgh50_trimmed.fastq ktrim=r k=23 mink=11 hdist=1 re f=/DATA/markop/bbmap/resources/adapters.fa tbo tpe maxns=0 trimq=20 qtrim=r maq=12
java -ea -Xmx230g -Xms230g -cp /DATA/markop/bbmap/current/ jgi.BBDuk -Xmx230g in=./input/Edinburgh50_1.fastq in2=./input/Edinburgh50_2.fastq out=./input/Edinburgh50_trimmed.fastq ktrim=r k=23 mink=11 hdist=1 ref=/DATA/markop/bbm ap/resources/adapters.fa tbo tpe maxns=0 trimq=20 qtrim=r maq=12
Executing jgi.BBDuk [-Xmx230g, in=./input/Edinburgh50_1.fastq, in2=./input/Edinburgh50_2.fastq, out=./input/Edinburgh50_trimmed.fastq, ktrim=r, k=23, mink=11, hdist=1, ref=/DATA/markop/bbmap/resources/adapters.fa, tbo, tpe, maxn s=0, trimq=20, qtrim=r, maq=12]
Version 38.34
maskMiddle was disabled because useShortKmers=true
0.049 seconds.
Initial:
Memory: max=236670m, total=236670m, free=229262m, used=7408m
Added 217045 kmers; time: 0.166 seconds.
Memory: max=236670m, total=236670m, free=216913m, used=19757m
Input is being processed as paired
Started output streams: 0.042 seconds.
Processing time: 1472.406 seconds.
Input: 315115950 reads 15755797500 bases.
QTrimmed: 64349819 reads (20.42%) 1151035751 bases (7.31%)
KTrimmed: 277964 reads (0.09%) 5268690 bases (0.03%)
Trimmed by overlap: 33102 reads (0.01%) 152958 bases (0.00%)
Low quality discards: 1013198 reads (0.32%) 46552569 bases (0.30%)
Total Removed: 7001884 reads (2.22%) 1203009968 bases (7.64%)
Result: 308114066 reads (97.78%) 14552787532 bases (92.36%)
Time: 1472.621 seconds.
Reads Processed: 315m 213.98k reads/sec
Bases Processed: 15755m 10.70m bases/sec
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbduk.sh -Xmx230g in=./input/Edinburgh75_1.fastq in2=./input/Edinburgh75_2.fastq out=./input/Edinburgh75_trimmed.fastq ktrim=r k=23 mink=11 hdist=1 re f=/DATA/markop/bbmap/resources/adapters.fa tbo tpe maxns=0 trimq=20 qtrim=r maq=12
java -ea -Xmx230g -Xms230g -cp /DATA/markop/bbmap/current/ jgi.BBDuk -Xmx230g in=./input/Edinburgh75_1.fastq in2=./input/Edinburgh75_2.fastq out=./input/Edinburgh75_trimmed.fastq ktrim=r k=23 mink=11 hdist=1 ref=/DATA/markop/bbm ap/resources/adapters.fa tbo tpe maxns=0 trimq=20 qtrim=r maq=12
Executing jgi.BBDuk [-Xmx230g, in=./input/Edinburgh75_1.fastq, in2=./input/Edinburgh75_2.fastq, out=./input/Edinburgh75_trimmed.fastq, ktrim=r, k=23, mink=11, hdist=1, ref=/DATA/markop/bbmap/resources/adapters.fa, tbo, tpe, maxn s=0, trimq=20, qtrim=r, maq=12]
Version 38.34
maskMiddle was disabled because useShortKmers=true
0.043 seconds.
Initial:
Memory: max=236670m, total=236670m, free=229262m, used=7408m
Added 217045 kmers; time: 0.156 seconds.
Memory: max=236670m, total=236670m, free=215679m, used=20991m
Input is being processed as paired
Started output streams: 0.046 seconds.
Processing time: 2292.027 seconds.
Input: 413862014 reads 31039651050 bases.
QTrimmed: 34224918 reads (8.27%) 747146144 bases (2.41%)
KTrimmed: 5281312 reads (1.28%) 326923182 bases (1.05%)
Trimmed by overlap: 1829354 reads (0.44%) 8825636 bases (0.03%)
Low quality discards: 3994226 reads (0.97%) 275900382 bases (0.89%)
Total Removed: 9462538 reads (2.29%) 1358795344 bases (4.38%)
Result: 404399476 reads (97.71%) 29680855706 bases (95.62%)
Time: 2292.235 seconds.
Reads Processed: 413m 180.55k reads/sec
Bases Processed: 31039m 13.54m bases/sec
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ #Remove small contaminants
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbduk.sh -Xmx230g in=./input/SUSPHIRE_trimmed.fastq out=./input/SUSPHIRE_filtered.fastq k=31 ref=/DATA/markop/bbmap/resources/sequencing_artifacts.fa. gz,/DATA/markop/bbmap/resources/phix174_ill.ref.fa.gz
java -ea -Xmx230g -Xms230g -cp /DATA/markop/bbmap/current/ jgi.BBDuk -Xmx230g in=./input/SUSPHIRE_trimmed.fastq out=./input/SUSPHIRE_filtered.fastq k=31 ref=/DATA/markop/bbmap/resources/sequencing_artifacts.fa.gz,/DATA/markop/bb map/resources/phix174_ill.ref.fa.gz
Executing jgi.BBDuk [-Xmx230g, in=./input/SUSPHIRE_trimmed.fastq, out=./input/SUSPHIRE_filtered.fastq, k=31, ref=/DATA/markop/bbmap/resources/sequencing_artifacts.fa.gz,/DATA/markop/bbmap/resources/phix174_ill.ref.fa.gz]
Version 38.34
0.039 seconds.
Initial:
Memory: max=236670m, total=236670m, free=228027m, used=8643m
Added 92358 kmers; time: 0.190 seconds.
Memory: max=236670m, total=236670m, free=216913m, used=19757m
Input is being processed as paired
Started output streams: 0.012 seconds.
Processing time: 2946.316 seconds.
Input: 663387562 reads 91912437691 bases.
Contaminants: 752 reads (0.00%) 81986 bases (0.00%)
Total Removed: 752 reads (0.00%) 81986 bases (0.00%)
Result: 663386810 reads (100.00%) 91912355705 bases (100.00%)
Time: 2946.524 seconds.
Reads Processed: 663m 225.14k reads/sec
Bases Processed: 91912m 31.19m bases/sec
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbduk.sh -Xmx230g in=./input/Edinburgh50_trimmed.fastq out=./input/Edinburgh50_filtered.fastq k=31 ref=/DATA/markop/bbmap/resources/sequencing_artifac ts.fa.gz,/DATA/markop/bbmap/resources/phix174_ill.ref.fa.gz
java -ea -Xmx230g -Xms230g -cp /DATA/markop/bbmap/current/ jgi.BBDuk -Xmx230g in=./input/Edinburgh50_trimmed.fastqout=./input/Edinburgh50_filtered.fastq k=31 ref=/DATA/markop/bbmap/resources/sequencing_artifacts.fa.gz,/DATA/mar kop/bbmap/resources/phix174_ill.ref.fa.gz
Executing jgi.BBDuk [-Xmx230g, in=./input/Edinburgh50_trimmed.fastq, out=./input/Edinburgh50_filtered.fastq, k=31, ref=/DATA/markop/bbmap/resources/sequencing_artifacts.fa.gz,/DATA/markop/bbmap/resources/phix174_ill.ref.fa.gz]
Version 38.34
0.036 seconds.
Initial:
Memory: max=236670m, total=236670m, free=230496m, used=6174m
Added 92358 kmers; time: 0.196 seconds.
Memory: max=236670m, total=236670m, free=220618m, used=16052m
Input is being processed as paired
Started output streams: 0.012 seconds.
Processing time: 640.881 seconds.
Input: 308114066 reads 14552787532 bases.
Contaminants: 0 reads (0.00%) 0 bases (0.00%)
Total Removed: 0 reads (0.00%) 0 bases (0.00%)
Result: 308114066 reads (100.00%) 14552787532 bases (100.00%)
Time: 641.093 seconds.
Reads Processed: 308m 480.61k reads/sec
Bases Processed: 14552m 22.70m bases/sec
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbduk.sh -Xmx230g in=./input/Edinburgh75_trimmed.fastq out=./input/Edinburgh75_filtered.fastq k=31 ref=/DATA/markop/bbmap/resources/sequencing_artifac ts.fa.gz,/DATA/markop/bbmap/resources/phix174_ill.ref.fa.gz
java -ea -Xmx230g -Xms230g -cp /DATA/markop/bbmap/current/ jgi.BBDuk -Xmx230g in=./input/Edinburgh75_trimmed.fastqout=./input/Edinburgh75_filtered.fastq k=31 ref=/DATA/markop/bbmap/resources/sequencing_artifacts.fa.gz,/DATA/mar kop/bbmap/resources/phix174_ill.ref.fa.gz
Executing jgi.BBDuk [-Xmx230g, in=./input/Edinburgh75_trimmed.fastq, out=./input/Edinburgh75_filtered.fastq, k=31, ref=/DATA/markop/bbmap/resources/sequencing_artifacts.fa.gz,/DATA/markop/bbmap/resources/phix174_ill.ref.fa.gz]
Version 38.34
0.038 seconds.
Initial:
Memory: max=236670m, total=236670m, free=229262m, used=7408m
Added 92358 kmers; time: 0.207 seconds.
Memory: max=236670m, total=236670m, free=216913m, used=19757m
Input is being processed as paired
Started output streams: 0.012 seconds.
Processing time: 1322.411 seconds.
Input: 404399476 reads 29680855706 bases.
Contaminants: 92 reads (0.00%) 4785 bases (0.00%)
Total Removed: 92 reads (0.00%) 4785 bases (0.00%)
Result: 404399384 reads (100.00%) 29680850921 bases (100.00%)
Time: 1322.633 seconds.
Reads Processed: 404m 305.75k reads/sec
Bases Processed: 29680m 22.44m bases/sec
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /home/administrator/Software/SPAdes-3.13.1-Linux/bin/spades.py \
> --only-error-correction \
> -m 230 \
> -t 32 \
> -o ./input \
> --pe1-fr --pe2-fr --pe3-fr \
> --pe1-12 ./input/SUSPHIRE_filtered.fastq \
> --pe2-12 ./input/Edinburgh50_filtered.fastq \
> --pe3-12 ./input/Edinburgh75_filtered.fastq
Command line: /home/administrator/Software/SPAdes-3.13.1-Linux/bin/spades.py --only-error-correction -m 230 -t 32 -o /DATA/markop/Pcitri_rnaspades_alldata/input --pe1-fr --pe2-fr --pe3-fr --pe1-12 /DATA/markop/Pcitri_rnaspades_alldata/input/SUSPHIRE_filtered.fastq --pe2-12 /DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh50_filtered.fastq --pe3-12 /DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh75_filtered.fastq
System information:
SPAdes version: 3.13.1
Python version: 2.7.12
OS: Linux-4.13.0-41-generic-x86_64-with-LinuxMint-18.2-sonya
Output dir: /DATA/markop/Pcitri_rnaspades_alldata/input
Mode: ONLY read error correction (without assembling)
Debug mode is turned OFF
Dataset parameters:
Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset)
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: not specified
right reads: not specified
interlaced reads: ['/DATA/markop/Pcitri_rnaspades_alldata/input/SUSPHIRE_filtered.fastq']
single reads: not specified
merged reads: not specified
Library number: 2, library type: paired-end
orientation: fr
left reads: not specified
right reads: not specified
interlaced reads: ['/DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh50_filtered.fastq']
single reads: not specified
merged reads: not specified
Library number: 3, library type: paired-end
orientation: fr
left reads: not specified
right reads: not specified
interlaced reads: ['/DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh75_filtered.fastq']
single reads: not specified
merged reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed
Other parameters:
Dir for temp files: /DATA/markop/Pcitri_rnaspades_alldata/input/tmp
Threads: 32
Memory limit (in Gb): 230
======= SPAdes pipeline started. Log can be found here: /DATA/markop/Pcitri_rnaspades_alldata/input/spades.log
== Splitting /DATA/markop/Pcitri_rnaspades_alldata/input/SUSPHIRE_filtered.fastq into left and right reads (in /DATA/markop/Pcitri_rnaspades_alldata/input/split_input directory)
== Splitting /DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh50_filtered.fastq into left and right reads (in /DATA/markop/Pcitri_rnaspades_alldata/input/split_input directory)
== Splitting /DATA/markop/Pcitri_rnaspades_alldata/input/Edinburgh75_filtered.fastq into left and right reads (in /DATA/markop/Pcitri_rnaspades_alldata/input/split_input directory)
===== Read error correction started.
== Running read error correction tool: /home/administrator/Software/SPAdes-3.13.1-Linux/bin/spades-hammer /DATA/markop/Pcitri_rnaspades_alldata/input/corrected/configs/config.info
0:00:00.000 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from refs/heads/spades_3.13.1, git revision 9a9d54db2ff9abaac718155bf74c12ec9464e8ca
0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /DATA/markop/Pcitri_rnaspades_alldata/input/corrected/configs/config.info
0:00:00.002 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 32
0:00:00.002 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 230 Gb
0:00:00.002 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset
0:00:00.011 4M / 4M INFO General (main.cpp : 92) Determined value is 33
0:00:00.011 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.011 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.012 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
0:00:00.012 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 512 files using 32 threads. This might take a while.
0:00:00.013 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 10000
0:00:00.013 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.39579 Gb
0:00:00.013 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072
0:00:00.122 17G / 17G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/SUSPHIRE_filtered_1.fastq
0:00:59.637 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 7551826 reads
0:01:57.064 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 15099419 reads
0:02:58.294 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 22632325 reads
0:03:58.434 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 30111488 reads
0:05:00.866 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 37626949 reads
0:06:04.349 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 45207512 reads
0:07:03.266 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 52764527 reads
0:08:04.166 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 60447827 reads
0:09:05.019 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 68064494 reads
0:10:06.500 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 75612315 reads
0:11:08.465 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 83161170 reads
0:12:09.625 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 90758682 reads
0:18:10.582 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 136365190 reads
0:36:45.438 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 275373560 reads
0:44:21.558 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/SUSPHIRE_filtered_2.fastq
1:11:44.448 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 537165579 reads
1:28:54.258 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/Edinburgh50_filtered_1.fastq
1:40:06.249 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/Edinburgh50_filtered_2.fastq
1:52:30.932 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/Edinburgh75_filtered_1.fastq
2:01:45.259 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 107) Processed 1078169479 reads
2:10:02.224 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/Edinburgh75_filtered_2.fastq
2:27:23.453 17G / 18G INFO K-mer Splitting (kmer_data.cpp : 112) Total 1375900260 reads processed
2:27:25.041 128M / 18G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
2:53:47.489 128M / 18G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2665835484 kmers in total.
2:53:47.489 128M / 18G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
2:54:06.518 128M / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
2:55:53.937 1G / 18G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
2:58:15.092 1G / 18G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1236163304 bytes occupied (3.70965 bits per kmer).
2:58:15.096 1G / 18G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order
3:00:14.669 41G / 41G INFO General (main.cpp : 148) Clustering Hamming graph.
4:01:51.554 41G / 41G INFO General (main.cpp : 155) Extracting clusters
4:46:10.114 41G / 97G INFO General (main.cpp : 167) Clustering done. Total clusters: 963678659
4:46:11.913 21G / 97G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while.
4:46:45.852 80G / 97G INFO K-mer Counting (kmer_data.cpp : 382) Processing /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/SUSPHIRE_filtered_1.fastq
5:46:29.452 80G / 97G INFO K-mer Counting (kmer_data.cpp : 382) Processing /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/SUSPHIRE_filtered_2.fastq
6:43:49.562 80G / 97G INFO K-mer Counting (kmer_data.cpp : 382) Processing /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/Edinburgh50_filtered_1.fastq
6:51:27.922 80G / 97G INFO K-mer Counting (kmer_data.cpp : 382) Processing /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/Edinburgh50_filtered_2.fastq
6:58:38.802 80G / 97G INFO K-mer Counting (kmer_data.cpp : 382) Processing /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/Edinburgh75_filtered_1.fastq
7:15:33.108 80G / 97G INFO K-mer Counting (kmer_data.cpp : 382) Processing /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/Edinburgh75_filtered_2.fastq
7:32:09.314 80G / 97G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing.
7:32:21.272 80G / 97G INFO K-mer Counting (kmer_data.cpp : 403) There are 2665835484 kmers in total. Among them 1629294690 (61.1176%) are singletons.
7:32:21.272 80G / 97G INFO General (main.cpp : 173) Subclustering Hamming graph
9:41:00.740 80G / 97G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 105389 non-read kmers were generated.
9:41:00.740 80G / 97G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics:
9:41:00.740 80G / 97G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 816331828. Among them 387596852 (47.4803%) are good
9:41:00.740 80G / 97G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 11642560. Among them 11608386 (99.7065%) are good
9:41:00.740 80G / 97G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 187925135. Among them 142141957 (75.6375%) are good
9:41:00.740 80G / 97G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 9.84488 kmers
9:41:00.740 80G / 97G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.35441
9:41:00.740 80G / 97G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 541347195
9:41:00.740 80G / 97G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.910902,0.0286632,0.028672,0.031763),(0.0368107,0.908562,0.0195257,0.0351015),(0.0326911,0.0189579,0.909382,0.0389691),(0.0304214,0.0285475,0.0285302,0.912501))
9:41:01.902 80G / 97G INFO General (main.cpp : 178) Finished clustering.
9:41:01.908 80G / 97G INFO General (main.cpp : 197) Starting solid k-mers expansion in 32 threads.
11:17:59.406 80G / 97G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 262811718 new k-mers.
12:54:22.502 80G / 97G INFO General (main.cpp : 218) Solid k-mers iteration 1 produced 22818263 new k-mers.
14:31:21.390 80G / 97G INFO General (main.cpp : 218) Solid k-mers iteration 2 produced 1694115 new k-mers.
16:07:14.730 80G / 97G INFO General (main.cpp : 218) Solid k-mers iteration 3 produced 227983 new k-mers.
17:42:51.650 80G / 97G INFO General (main.cpp : 218) Solid k-mers iteration 4 produced 46172 new k-mers.
19:19:05.346 80G / 97G INFO General (main.cpp : 218) Solid k-mers iteration 5 produced 14599 new k-mers.
20:55:46.246 80G / 97G INFO General (main.cpp : 218) Solid k-mers iteration 6 produced 4875 new k-mers.
22:31:40.518 80G / 97G INFO General (main.cpp : 218) Solid k-mers iteration 7 produced 1774 new k-mers.
24:07:36.254 80G / 97G INFO General (main.cpp : 218) Solid k-mers iteration 8 produced 604 new k-mers.
25:43:22.014 80G / 97G INFO General (main.cpp : 218) Solid k-mers iteration 9 produced 304 new k-mers.
27:19:10.398 80G / 97G INFO General (main.cpp : 218) Solid k-mers iteration 10 produced 69 new k-mers.
28:54:48.186 80G / 97G INFO General (main.cpp : 218) Solid k-mers iteration 11 produced 0 new k-mers.
28:54:48.187 80G / 97G INFO General (main.cpp : 222) Solid k-mers finalized
28:54:48.192 80G / 97G INFO General (hammer_tools.cpp : 220) Starting read correction in 32 threads.
28:54:48.192 80G / 97G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/SUSPHIRE_filtered_1.fastq and /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/SUSPHIRE_filtered_2.fastq
28:55:10.793 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads.
28:55:36.575 84G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 0
28:55:42.569 84G / 97G INFO General (hammer_tools.cpp : 185) Written batch 0
28:56:18.435 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads.
28:56:44.274 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 1
28:56:50.497 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 1
28:57:28.314 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 3200000 reads.
28:57:54.855 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 2
28:58:01.125 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 2
28:58:38.756 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 3200000 reads.
28:59:05.046 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 3
28:59:11.188 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 3
28:59:48.221 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 3200000 reads.
29:00:13.602 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 4
29:00:19.733 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 4
29:00:57.508 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 3200000 reads.
29:01:22.922 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 5
29:01:29.234 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 5
29:02:05.940 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 3200000 reads.
29:02:31.851 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 6
29:02:38.208 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 6
29:03:16.627 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 3200000 reads.
29:03:42.662 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 7
29:03:49.189 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 7
29:04:27.173 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 3200000 reads.
29:04:53.458 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 8
29:05:00.697 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 8
29:05:39.014 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 3200000 reads.
29:06:05.972 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 9
29:06:13.590 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 9
29:06:51.540 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 10 of 3200000 reads.
29:07:16.424 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 10
29:07:22.618 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 10
29:08:00.868 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 11 of 3200000 reads.
29:08:25.835 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 11
29:08:31.793 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 11
29:09:10.536 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 12 of 3200000 reads.
29:09:37.151 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 12
29:09:43.147 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 12
29:10:20.554 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 13 of 3200000 reads.
29:10:45.796 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 13
29:10:51.814 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 13
29:11:30.390 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 14 of 3200000 reads.
29:11:55.591 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 14
29:12:01.791 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 14
29:12:40.207 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 15 of 3200000 reads.
29:13:05.683 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 15
29:13:11.835 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 15
29:13:50.770 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 16 of 3200000 reads.
29:14:16.032 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 16
29:14:22.720 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 16
29:15:00.455 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 17 of 3200000 reads.
29:15:25.174 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 17
29:15:32.452 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 17
29:16:10.469 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 18 of 3200000 reads.
29:16:35.203 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 18
29:16:41.280 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 18
29:17:17.932 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 19 of 3200000 reads.
29:17:42.327 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 19
29:17:48.294 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 19
29:18:27.265 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 20 of 3200000 reads.
29:18:53.770 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 20
29:18:59.725 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 20
29:19:37.563 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 21 of 3200000 reads.
29:20:03.130 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 21
29:20:09.178 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 21
29:20:47.678 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 22 of 3200000 reads.
29:21:14.034 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 22
29:21:20.211 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 22
29:21:57.870 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 23 of 3200000 reads.
29:22:25.069 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 23
29:22:31.163 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 23
29:23:09.370 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 24 of 3200000 reads.
29:23:34.520 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 24
29:23:40.571 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 24
29:24:18.230 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 25 of 3200000 reads.
29:24:43.172 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 25
29:24:49.202 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 25
29:25:27.810 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 26 of 3200000 reads.
29:25:53.870 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 26
29:25:59.959 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 26
29:26:39.022 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 27 of 3200000 reads.
29:27:04.675 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 27
29:27:11.230 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 27
29:27:48.412 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 28 of 3200000 reads.
29:28:13.243 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 28
29:28:20.324 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 28
29:28:57.766 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 29 of 3200000 reads.
29:29:22.226 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 29
29:29:28.200 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 29
29:30:06.280 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 30 of 3200000 reads.
29:30:31.194 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 30
29:30:37.113 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 30
29:31:16.460 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 31 of 3200000 reads.
29:31:42.743 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 31
29:31:48.682 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 31
29:32:26.710 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 32 of 3200000 reads.
29:32:52.021 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 32
29:32:57.950 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 32
29:33:37.421 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 33 of 3200000 reads.
29:34:02.719 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 33
29:34:08.672 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 33
29:34:46.662 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 34 of 3200000 reads.
29:35:11.878 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 34
29:35:17.999 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 34
29:35:57.628 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 35 of 3200000 reads.
29:36:22.571 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 35
29:36:28.980 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 35
29:37:07.207 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 36 of 3200000 reads.
29:37:34.022 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 36
29:37:40.600 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 36
29:38:20.724 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 37 of 3200000 reads.
29:38:45.843 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 37
29:38:52.520 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 37
29:39:30.826 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 38 of 3200000 reads.
29:39:57.297 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 38
29:40:04.057 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 38
29:40:45.119 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 39 of 3200000 reads.
29:41:12.089 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 39
29:41:19.186 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 39
29:41:57.440 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 40 of 3200000 reads.
29:42:22.120 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 40
29:42:28.234 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 40
29:43:08.355 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 41 of 3200000 reads.
29:43:33.292 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 41
29:43:39.247 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 41
29:44:17.070 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 42 of 3200000 reads.
29:44:43.065 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 42
29:44:49.017 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 42
29:45:29.083 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 43 of 3200000 reads.
29:45:55.375 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 43
29:46:01.334 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 43
29:46:40.190 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 44 of 3200000 reads.
29:47:04.678 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 44
29:47:10.721 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 44
29:47:51.399 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 45 of 3200000 reads.
29:48:16.553 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 45
29:48:22.623 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 45
29:49:01.598 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 46 of 3200000 reads.
29:49:27.263 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 46
29:49:33.366 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 46
29:50:13.417 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 47 of 3200000 reads.
29:50:38.026 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 47
29:50:44.331 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 47
29:51:23.777 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 48 of 3200000 reads.
29:51:48.387 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 48
29:51:55.434 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 48
29:52:35.357 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 49 of 3200000 reads.
29:53:00.543 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 49
29:53:06.521 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 49
29:53:44.876 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 50 of 3200000 reads.
29:54:10.807 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 50
29:54:16.754 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 50
29:54:56.784 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 51 of 3200000 reads.
29:55:23.341 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 51
29:55:29.388 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 51
29:56:10.072 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 52 of 3200000 reads.
29:56:37.273 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 52
29:56:43.331 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 52
29:57:23.380 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 53 of 3200000 reads.
29:57:48.311 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 53
29:57:54.283 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 53
29:58:34.985 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 54 of 3200000 reads.
29:59:00.495 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 54
29:59:06.457 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 54
29:59:47.184 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 55 of 3200000 reads.
30:00:12.946 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 55
30:00:19.127 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 55
30:00:58.322 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 56 of 3200000 reads.
30:01:23.691 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 56
30:01:29.870 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 56
30:02:10.271 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 57 of 3200000 reads.
30:02:35.634 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 57
30:02:42.315 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 57
30:03:21.159 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 58 of 3200000 reads.
30:03:47.426 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 58
30:03:54.682 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 58
30:04:33.644 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 59 of 3200000 reads.
30:04:58.799 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 59
30:05:04.794 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 59
30:05:44.837 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 60 of 3200000 reads.
30:06:10.099 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 60
30:06:16.001 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 60
30:06:54.842 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 61 of 3200000 reads.
30:07:20.389 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 61
30:07:26.289 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 61
30:08:06.726 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 62 of 3200000 reads.
30:08:32.933 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 62
30:08:38.991 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 62
30:09:18.468 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 63 of 3200000 reads.
30:09:45.490 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 63
30:09:51.512 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 63
30:10:32.413 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 64 of 3200000 reads.
30:11:00.105 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 64
30:11:06.184 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 64
30:11:44.054 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 65 of 3200000 reads.
30:12:09.803 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 65
30:12:15.940 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 65
30:12:57.247 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 66 of 3200000 reads.
30:13:24.485 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 66
30:13:30.847 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 66
30:14:09.024 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 67 of 3200000 reads.
30:14:35.593 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 67
30:14:42.045 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 67
30:15:23.103 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 68 of 3200000 reads.
30:15:48.614 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 68
30:15:55.504 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 68
30:16:34.213 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 69 of 3200000 reads.
30:17:00.654 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 69
30:17:07.849 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 69
30:17:49.140 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 70 of 3200000 reads.
30:18:15.525 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 70
30:18:21.601 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 70
30:18:59.805 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 71 of 3200000 reads.
30:19:25.915 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 71
30:19:31.870 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 71
30:20:12.699 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 72 of 3200000 reads.
30:20:38.467 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 72
30:20:44.439 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 72
30:21:23.950 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 73 of 3200000 reads.
30:21:51.502 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 73
30:21:57.469 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 73
30:22:37.851 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 74 of 3200000 reads.
30:23:04.371 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 74
30:23:10.419 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 74
30:23:50.619 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 75 of 3200000 reads.
30:24:18.413 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 75
30:24:24.595 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 75
30:25:05.442 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 76 of 3200000 reads.
30:25:30.686 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 76
30:25:37.306 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 76
30:26:17.642 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 77 of 3200000 reads.
30:26:44.438 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 77
30:26:51.331 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 77
30:27:32.426 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 78 of 3200000 reads.
30:27:58.684 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 78
30:28:05.925 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 78
30:28:46.153 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 79 of 3200000 reads.
30:29:11.885 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 79
30:29:17.927 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 79
30:29:59.083 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 80 of 3200000 reads.
30:30:25.125 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 80
30:30:31.317 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 80
30:31:12.327 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 81 of 3200000 reads.
30:31:39.592 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 81
30:31:45.736 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 81
30:32:26.763 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 82 of 3200000 reads.
30:32:52.350 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 82
30:32:58.319 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 82
30:33:39.755 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 83 of 3200000 reads.
30:34:05.778 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 83
30:34:11.758 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 83
30:34:52.431 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 84 of 3200000 reads.
30:35:19.278 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 84
30:35:25.423 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 84
30:36:05.566 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 85 of 3200000 reads.
30:36:32.644 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 85
30:36:38.795 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 85
30:37:20.660 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 86 of 3200000 reads.
30:37:46.912 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 86
30:37:53.119 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 86
30:38:33.211 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 87 of 3200000 reads.
30:39:00.862 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 87
30:39:07.198 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 87
30:39:48.978 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 88 of 3200000 reads.
30:40:14.197 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 88
30:40:20.912 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 88
30:41:01.565 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 89 of 3200000 reads.
30:41:27.921 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 89
30:41:35.276 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 89
30:42:18.065 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 90 of 3200000 reads.
30:42:45.540 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 90
30:42:51.767 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 90
30:43:31.632 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 91 of 3200000 reads.
30:43:57.436 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 91
30:44:03.479 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 91
30:44:45.188 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 92 of 3200000 reads.
30:45:11.105 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 92
30:45:17.024 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 92
30:45:57.143 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 93 of 3200000 reads.
30:46:23.520 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 93
30:46:29.560 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 93
30:47:10.308 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 94 of 3200000 reads.
30:47:36.767 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 94
30:47:42.841 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 94
30:48:23.384 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 95 of 3200000 reads.
30:48:49.022 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 95
30:48:55.257 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 95
30:49:36.209 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 96 of 3200000 reads.
30:50:02.168 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 96
30:50:08.417 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 96
30:50:48.793 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 97 of 3200000 reads.
30:51:15.002 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 97
30:51:21.586 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 97
30:52:03.229 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 98 of 3200000 reads.
30:52:29.672 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 98
30:52:36.871 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 98
30:53:17.670 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 99 of 3200000 reads.
30:53:44.521 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 99
30:53:51.432 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 99
30:54:33.130 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 100 of 3200000 reads.
30:55:01.026 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 100
30:55:07.431 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 100
30:55:46.316 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 101 of 3200000 reads.
30:56:11.942 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 101
30:56:17.888 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 101
30:56:57.976 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 102 of 3200000 reads.
30:57:25.071 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 102
30:57:31.063 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 102
30:58:07.248 85G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 103 of 2093405 reads.
30:58:25.665 85G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 103
30:58:29.554 85G / 97G INFO General (hammer_tools.cpp : 185) Written batch 103
30:58:32.596 80G / 97G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/Edinburgh50_filtered_1.fastq and /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/Edinburgh50_filtered_2.fastq
30:58:55.574 82G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads.
30:59:02.054 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 0
30:59:05.756 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 0
30:59:19.788 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads.
30:59:26.454 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 1
30:59:30.534 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 1
30:59:50.103 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 3200000 reads.
30:59:56.669 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 2
31:00:00.643 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 2
31:00:10.730 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 3200000 reads.
31:00:17.324 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 3
31:00:21.183 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 3
31:00:57.275 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 3200000 reads.
31:01:03.875 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 4
31:01:07.823 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 4
31:01:18.393 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 3200000 reads.
31:01:24.702 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 5
31:01:28.669 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 5
31:02:02.429 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 3200000 reads.
31:02:08.876 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 6
31:02:12.745 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 6
31:02:22.158 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 3200000 reads.
31:02:28.900 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 7
31:02:33.190 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 7
31:03:06.389 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 3200000 reads.
31:03:12.607 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 8
31:03:16.426 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 8
31:03:26.268 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 3200000 reads.
31:03:32.521 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 9
31:03:36.497 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 9
31:04:10.088 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 10 of 3200000 reads.
31:04:16.664 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 10
31:04:21.233 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 10
31:04:30.839 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 11 of 3200000 reads.
31:04:37.164 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 11
31:04:41.142 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 11
31:05:10.331 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 12 of 3200000 reads.
31:05:16.789 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 12
31:05:20.637 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 12
31:05:30.234 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 13 of 3200000 reads.
31:05:37.122 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 13
31:05:41.094 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 13
31:06:12.333 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 14 of 3200000 reads.
31:06:18.754 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 14
31:06:22.603 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 14
31:06:32.063 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 15 of 3200000 reads.
31:06:38.484 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 15
31:06:42.385 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 15
31:07:11.166 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 16 of 3200000 reads.
31:07:17.882 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 16
31:07:21.718 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 16
31:07:31.584 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 17 of 3200000 reads.
31:07:37.982 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 17
31:07:42.206 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 17
31:08:14.556 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 18 of 3200000 reads.
31:08:20.856 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 18
31:08:24.665 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 18
31:08:34.348 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 19 of 3200000 reads.
31:08:40.730 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 19
31:08:44.893 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 19
31:09:15.123 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 20 of 3200000 reads.
31:09:22.052 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 20
31:09:26.027 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 20
31:09:35.740 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 21 of 3200000 reads.
31:09:42.101 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 21
31:09:45.933 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 21
31:10:21.821 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 22 of 3200000 reads.
31:10:28.048 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 22
31:10:31.849 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 22
31:10:42.922 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 23 of 3200000 reads.
31:10:49.488 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 23
31:10:53.340 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 23
31:11:20.111 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 24 of 3200000 reads.
31:11:26.697 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 24
31:11:30.526 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 24
31:11:40.559 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 25 of 3200000 reads.
31:11:47.137 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 25
31:11:51.413 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 25
31:12:25.322 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 26 of 3200000 reads.
31:12:31.762 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 26
31:12:35.599 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 26
31:12:45.656 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 27 of 3200000 reads.
31:12:52.125 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 27
31:12:55.987 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 27
31:13:25.983 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 28 of 3200000 reads.
31:13:32.662 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 28
31:13:36.669 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 28
31:13:46.214 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 29 of 3200000 reads.
31:13:52.755 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 29
31:13:56.679 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 29
31:14:32.473 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 30 of 3200000 reads.
31:14:39.135 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 30
31:14:42.983 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 30
31:14:53.792 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 31 of 3200000 reads.
31:15:00.428 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 31
31:15:04.350 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 31
31:15:27.518 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 32 of 3200000 reads.
31:15:34.236 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 32
31:15:38.101 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 32
31:15:47.681 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 33 of 3200000 reads.
31:15:54.106 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 33
31:15:57.926 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 33
31:16:33.590 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 34 of 3200000 reads.
31:16:40.170 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 34
31:16:44.000 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 34
31:16:54.864 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 35 of 3200000 reads.
31:17:01.297 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 35
31:17:05.484 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 35
31:17:30.147 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 36 of 3200000 reads.
31:17:36.637 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 36
31:17:40.572 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 36
31:17:50.269 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 37 of 3200000 reads.
31:17:56.742 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 37
31:18:00.554 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 37
31:18:38.338 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 38 of 3200000 reads.
31:18:44.653 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 38
31:18:48.519 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 38
31:18:57.909 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 39 of 3200000 reads.
31:19:04.779 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 39
31:19:09.657 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 39
31:19:38.772 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 40 of 3200000 reads.
31:19:45.205 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 40
31:19:49.041 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 40
31:19:58.648 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 41 of 3200000 reads.
31:20:05.289 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 41
31:20:09.166 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 41
31:20:46.445 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 42 of 3200000 reads.
31:20:53.078 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 42
31:20:56.964 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 42
31:21:08.251 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 43 of 3200000 reads.
31:21:14.581 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 43
31:21:18.430 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 43
31:21:45.278 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 44 of 3200000 reads.
31:21:51.798 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 44
31:21:55.830 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 44
31:22:05.757 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 45 of 3200000 reads.
31:22:12.529 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 45
31:22:16.429 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 45
31:22:48.622 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 46 of 3200000 reads.
31:22:55.363 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 46
31:22:59.195 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 46
31:23:08.839 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 47 of 3200000 reads.
31:23:15.490 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 47
31:23:19.501 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 47
31:23:31.357 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 48 of 457033 reads.
31:23:32.359 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 48
31:23:32.929 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 48
31:23:35.051 80G / 97G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/Edinburgh75_filtered_1.fastq and /DATA/markop/Pcitri_rnaspades_alldata/input/split_input/Edinburgh75_filtered_2.fastq
31:24:00.759 82G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 3200000 reads.
31:24:12.210 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 0
31:24:17.043 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 0
31:24:46.474 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 1 of 3200000 reads.
31:24:58.080 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 1
31:25:02.314 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 1
31:25:30.614 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 2 of 3200000 reads.
31:25:42.669 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 2
31:25:47.753 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 2
31:26:18.015 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 3 of 3200000 reads.
31:26:29.692 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 3
31:26:34.011 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 3
31:27:03.431 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 4 of 3200000 reads.
31:27:15.117 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 4
31:27:19.787 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 4
31:27:50.234 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 5 of 3200000 reads.
31:28:01.766 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 5
31:28:06.029 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 5
31:28:34.664 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 6 of 3200000 reads.
31:28:46.422 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 6
31:28:51.115 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 6
31:29:21.711 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 7 of 3200000 reads.
31:29:33.108 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 7
31:29:37.312 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 7
31:29:58.508 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 8 of 3200000 reads.
31:30:10.143 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 8
31:30:14.392 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 8
31:30:27.192 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 9 of 3200000 reads.
31:30:39.017 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 9
31:30:43.950 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 9
31:31:20.482 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 10 of 3200000 reads.
31:31:34.527 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 10
31:31:38.812 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 10
31:32:09.922 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 11 of 3200000 reads.
31:32:24.602 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 11
31:32:28.863 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 11
31:32:57.608 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 12 of 3200000 reads.
31:33:13.370 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 12
31:33:18.168 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 12
31:33:48.675 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 13 of 3200000 reads.
31:34:01.041 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 13
31:34:05.240 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 13
31:34:36.423 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 14 of 3200000 reads.
31:34:49.164 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 14
31:34:54.187 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 14
31:35:24.114 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 15 of 3200000 reads.
31:35:35.620 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 15
31:35:39.870 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 15
31:36:09.748 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 16 of 3200000 reads.
31:36:21.561 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 16
31:36:26.131 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 16
31:36:58.078 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 17 of 3200000 reads.
31:37:09.947 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 17
31:37:14.165 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 17
31:37:42.966 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 18 of 3200000 reads.
31:37:55.051 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 18
31:37:59.298 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 18
31:38:13.712 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 19 of 3200000 reads.
31:38:25.494 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 19
31:38:29.814 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 19
31:38:58.082 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 20 of 3200000 reads.
31:39:09.578 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 20
31:39:13.772 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 20
31:39:44.538 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 21 of 3200000 reads.
31:39:55.862 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 21
31:40:00.253 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 21
31:40:30.195 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 22 of 3200000 reads.
31:40:41.497 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 22
31:40:45.755 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 22
31:41:17.257 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 23 of 3200000 reads.
31:41:28.659 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 23
31:41:32.867 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 23
31:42:01.125 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 24 of 3200000 reads.
31:42:12.485 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 24
31:42:16.714 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 24
31:42:30.838 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 25 of 3200000 reads.
31:42:42.088 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 25
31:42:46.486 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 25
31:43:18.513 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 26 of 3200000 reads.
31:43:29.741 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 26
31:43:33.998 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 26
31:44:03.745 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 27 of 3200000 reads.
31:44:15.323 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 27
31:44:19.663 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 27
31:44:51.783 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 28 of 3200000 reads.
31:45:02.890 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 28
31:45:07.153 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 28
31:45:37.611 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 29 of 3200000 reads.
31:45:49.219 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 29
31:45:53.871 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 29
31:46:19.516 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 30 of 3200000 reads.
31:46:31.400 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 30
31:46:35.673 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 30
31:46:50.608 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 31 of 3200000 reads.
31:47:04.586 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 31
31:47:09.448 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 31
31:47:38.437 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 32 of 3200000 reads.
31:47:52.117 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 32
31:47:56.420 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 32
31:48:26.194 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 33 of 3200000 reads.
31:48:41.022 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 33
31:48:45.417 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 33
31:49:17.148 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 34 of 3200000 reads.
31:49:28.448 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 34
31:49:32.677 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 34
31:50:04.702 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 35 of 3200000 reads.
31:50:16.951 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 35
31:50:21.551 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 35
31:50:53.527 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 36 of 3200000 reads.
31:51:05.134 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 36
31:51:09.615 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 36
31:51:40.283 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 37 of 3200000 reads.
31:51:51.831 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 37
31:51:56.555 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 37
31:52:26.309 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 38 of 3200000 reads.
31:52:37.199 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 38
31:52:41.422 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 38
31:52:58.805 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 39 of 3200000 reads.
31:53:10.366 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 39
31:53:14.611 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 39
31:53:28.170 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 40 of 3200000 reads.
31:53:39.414 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 40
31:53:43.671 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 40
31:54:27.571 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 41 of 3200000 reads.
31:54:39.461 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 41
31:54:43.705 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 41
31:55:13.844 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 42 of 3200000 reads.
31:55:25.078 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 42
31:55:29.327 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 42
31:56:00.063 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 43 of 3200000 reads.
31:56:11.488 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 43
31:56:15.718 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 43
31:56:47.035 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 44 of 3200000 reads.
31:56:58.221 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 44
31:57:02.480 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 44
31:57:17.861 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 45 of 3200000 reads.
31:57:29.728 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 45
31:57:34.017 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 45
31:58:03.960 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 46 of 3200000 reads.
31:58:15.457 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 46
31:58:19.972 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 46
31:58:52.334 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 47 of 3200000 reads.
31:59:03.730 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 47
31:59:07.978 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 47
31:59:41.603 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 48 of 3200000 reads.
31:59:52.926 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 48
31:59:57.146 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 48
32:00:29.781 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 49 of 3200000 reads.
32:00:41.396 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 49
32:00:45.669 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 49
32:01:18.199 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 50 of 3200000 reads.
32:01:29.382 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 50
32:01:33.661 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 50
32:02:06.738 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 51 of 3200000 reads.
32:02:18.034 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 51
32:02:22.307 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 51
32:02:54.329 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 52 of 3200000 reads.
32:03:07.034 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 52
32:03:11.258 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 52
32:03:43.519 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 53 of 3200000 reads.
32:03:59.291 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 53
32:04:03.915 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 53
32:04:36.182 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 54 of 3200000 reads.
32:04:50.314 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 54
32:04:54.554 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 54
32:05:26.425 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 55 of 3200000 reads.
32:05:41.173 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 55
32:05:46.162 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 55
32:06:17.388 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 56 of 3200000 reads.
32:06:29.640 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 56
32:06:33.879 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 56
32:07:06.549 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 57 of 3200000 reads.
32:07:18.920 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 57
32:07:23.742 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 57
32:07:56.167 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 58 of 3200000 reads.
32:08:07.315 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 58
32:08:11.497 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 58
32:08:43.137 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 59 of 3200000 reads.
32:08:54.868 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 59
32:08:59.480 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 59
32:09:32.495 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 60 of 3200000 reads.
32:09:43.894 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 60
32:09:48.162 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 60
32:10:21.908 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 61 of 3200000 reads.
32:10:33.466 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 61
32:10:37.698 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 61
32:11:10.993 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 62 of 3200000 reads.
32:11:22.514 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 62
32:11:26.773 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 62
32:11:30.215 83G / 97G INFO General (hammer_tools.cpp : 168) Prepared batch 63 of 599692 reads.
32:11:32.565 83G / 97G INFO General (hammer_tools.cpp : 175) Processed batch 63
32:11:33.371 83G / 97G INFO General (hammer_tools.cpp : 185) Written batch 63
32:11:35.359 80G / 97G INFO General (hammer_tools.cpp : 274) Correction done. Changed 74689591 bases in 55263781 reads.
32:11:35.359 80G / 97G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 135963462477.
32:11:43.933 128M / 97G INFO General (main.cpp : 255) Saving corrected dataset description to /DATA/markop/Pcitri_rnaspades_alldata/input/corrected/corrected.yaml
32:11:43.939 128M / 97G INFO General (main.cpp : 262) All done. Exiting.
== Compressing corrected reads (with pigz)
== Dataset description file was created: /DATA/markop/Pcitri_rnaspades_alldata/input/corrected/corrected.yaml
===== Read error correction finished.
* Corrected reads are in /DATA/markop/Pcitri_rnaspades_alldata/input/corrected/
======= SPAdes pipeline finished.
SPAdes log can be found here: /DATA/markop/Pcitri_rnaspades_alldata/input/spades.log
Thank you for using SPAdes!
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbmerge.sh -Xmx230g in1=./input/corrected/SUSPHIRE_filtered_1.00.0_0.cor.fastq.gz in2=./input/corrected/SUSPHIRE_filtered_2.00.0_0.cor.fastq.gz out=./input/SUSPHIRE_ecco_PE.fastq ecco mix vstrict adapters=default
java -ea -Xmx230g -Xms230g -cp /DATA/markop/bbmap/current/ jgi.BBMerge -Xmx230g in1=./input/corrected/SUSPHIRE_filtered_1.00.0_0.cor.fastq.gz in2=./input/corrected/SUSPHIRE_filtered_2.00.0_0.cor.fastq.gz out=./input/SUSPHIRE_ecco_PE.fastq ecco mix vstrict adapters=default
Executing jgi.BBMerge [-Xmx230g, in1=./input/corrected/SUSPHIRE_filtered_1.00.0_0.cor.fastq.gz, in2=./input/corrected/SUSPHIRE_filtered_2.00.0_0.cor.fastq.gz, out=./input/SUSPHIRE_ecco_PE.fastq, ecco, mix, vstrict, adapters=default]
Version 38.34
Revised arguments: [maxbad=4, margin=3, minqo=8, qualiters=2, ratiomode=t, flatmode=f, minentropy=52, minoverlap=12, minoverlap0=4, maxratio=0.05, ratiomargin=12, ratiooffset=0.5, ratiominoverlapreduction=4, efilter=2, pfilter=0.008, minsecondratio=0.16, minapproxoverlap=22, in1=./input/corrected/SUSPHIRE_filtered_1.00.0_0.cor.fastq.gz, in2=./input/corrected/SUSPHIRE_filtered_2.00.0_0.cor.fastq.gz, out=./input/SUSPHIRE_ecco_PE.fastq, ecco, mix, adapters=default]
Writing mergable reads interleaved.
Started output threads.
Total time: 2574.617 seconds.
Pairs: 328795403
Joined: 228323343 69.442%
Ambiguous: 100385153 30.531%
No Solution: 86907 0.026%
Too Short: 0 0.000%
Adapters Expected: 79124 0.012%
Adapters Found: 64843 0.010%
Errors Corrected: 8880345
Avg Insert: 184.1
Standard Deviation: 49.8
Mode: 167
Insert range: 35 - 289
90th percentile: 255
75th percentile: 222
50th percentile: 182
25th percentile: 145
10th percentile: 119
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbmerge.sh -Xmx230g in=./input/corrected/SUSPHIRE_filtered__unpaired.00.0_0.cor.fastq.gz out=./input/SUSPHIRE_ecco_SE.fastq ecco mix vstrict adapters=default
java -ea -Xmx230g -Xms230g -cp /DATA/markop/bbmap/current/ jgi.BBMerge -Xmx230g in=./input/corrected/SUSPHIRE_filtered__unpaired.00.0_0.cor.fastq.gz out=./input/SUSPHIRE_ecco_SE.fastq ecco mix vstrict adapters=default
Executing jgi.BBMerge [-Xmx230g, in=./input/corrected/SUSPHIRE_filtered__unpaired.00.0_0.cor.fastq.gz, out=./input/SUSPHIRE_ecco_SE.fastq, ecco, mix, vstrict, adapters=default]
Version 38.34
Revised arguments: [maxbad=4, margin=3, minqo=8, qualiters=2, ratiomode=t, flatmode=f, minentropy=52, minoverlap=12, minoverlap0=4, maxratio=0.05, ratiomargin=12, ratiooffset=0.5, ratiominoverlapreduction=4, efilter=2, pfilter=0.008, minsecondratio=0.16, minapproxoverlap=22, in=./input/corrected/SUSPHIRE_filtered__unpaired.00.0_0.cor.fastq.gz, out=./input/SUSPHIRE_ecco_SE.fastq, ecco, mix, adapters=default]
Writing mergable reads interleaved.
Started output threads.
Total time: 7.126 seconds.
Pairs: 1418786
Joined: 24 0.002%
Ambiguous: 1418746 99.997%
No Solution: 16 0.001%
Too Short: 0 0.000%
Adapters Expected: 23 0.001%
Adapters Found: 0 0.000%
Errors Corrected: 8
Avg Insert: 189.8
Standard Deviation: 37.2
Mode: 195
Insert range: 131 - 277
90th percentile: 243
75th percentile: 200
50th percentile: 179
25th percentile: 163
10th percentile: 136
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbmerge.sh -Xmx230g in1=./input/corrected/Edinburgh50_filtered_1.00.1_0.cor.fastq.gz in2=./input/corrected/Edinburgh50_filtered_2.00.1_0.cor.fastq.gz out=./input/Edinburgh50_ecco_PE.fastq ecco mix vstrict adapters=default
java -ea -Xmx230g -Xms230g -cp /DATA/markop/bbmap/current/ jgi.BBMerge -Xmx230g in1=./input/corrected/Edinburgh50_filtered_1.00.1_0.cor.fastq.gz in2=./input/corrected/Edinburgh50_filtered_2.00.1_0.cor.fastq.gz out=./input/Edinburgh50_ecco_PE.fastq ecco mix vstrict adapters=default
Executing jgi.BBMerge [-Xmx230g, in1=./input/corrected/Edinburgh50_filtered_1.00.1_0.cor.fastq.gz, in2=./input/corrected/Edinburgh50_filtered_2.00.1_0.cor.fastq.gz, out=./input/Edinburgh50_ecco_PE.fastq, ecco, mix, vstrict, adapters=default]
Version 38.34
Revised arguments: [maxbad=4, margin=3, minqo=8, qualiters=2, ratiomode=t, flatmode=f, minentropy=52, minoverlap=12, minoverlap0=4, maxratio=0.05, ratiomargin=12, ratiooffset=0.5, ratiominoverlapreduction=4, efilter=2, pfilter=0.008, minsecondratio=0.16, minapproxoverlap=22, in1=./input/corrected/Edinburgh50_filtered_1.00.1_0.cor.fastq.gz, in2=./input/corrected/Edinburgh50_filtered_2.00.1_0.cor.fastq.gz, out=./input/Edinburgh50_ecco_PE.fastq, ecco, mix, adapters=default]
Writing mergable reads interleaved.
Started output threads.
Total time: 561.432 seconds.
Pairs: 141794014
Joined: 1204313 0.849%
Ambiguous: 140587795 99.149%
No Solution: 1906 0.001%
Too Short: 0 0.000%
Adapters Expected: 4227 0.001%
Adapters Found: 565 0.000%
Errors Corrected: 1743
Avg Insert: 77.5
Standard Deviation: 8.8
Mode: 83
Insert range: 35 - 89
90th percentile: 86
75th percentile: 84
50th percentile: 80
25th percentile: 73
10th percentile: 65
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbmerge.sh -Xmx230g in=./input/corrected/Edinburgh50_filtered__unpaired.00.1_0.cor.fastq.gz out=./input/Edinburgh50_ecco_SE.fastq ecco mix vstrict adapters=default
java -ea -Xmx230g -Xms230g -cp /DATA/markop/bbmap/current/ jgi.BBMerge -Xmx230g in=./input/corrected/Edinburgh50_filtered__unpaired.00.1_0.cor.fastq.gz out=./input/Edinburgh50_ecco_SE.fastq ecco mix vstrict adapters=default
Executing jgi.BBMerge [-Xmx230g, in=./input/corrected/Edinburgh50_filtered__unpaired.00.1_0.cor.fastq.gz, out=./input/Edinburgh50_ecco_SE.fastq, ecco, mix, vstrict, adapters=default]
Version 38.34
Revised arguments: [maxbad=4, margin=3, minqo=8, qualiters=2, ratiomode=t, flatmode=f, minentropy=52, minoverlap=12, minoverlap0=4, maxratio=0.05, ratiomargin=12, ratiooffset=0.5, ratiominoverlapreduction=4, efilter=2, pfilter=0.008, minsecondratio=0.16, minapproxoverlap=22, in=./input/corrected/Edinburgh50_filtered__unpaired.00.1_0.cor.fastq.gz, out=./input/Edinburgh50_ecco_SE.fastq, ecco, mix, adapters=default]
Writing mergable reads interleaved.
Started output threads.
Total time: 12.628 seconds.
Pairs: 5811999
Joined: 23 0.000%
Ambiguous: 5811975 100.000%
No Solution: 1 0.000%
Too Short: 0 0.000%
Adapters Expected: 4 0.000%
Adapters Found: 2 0.000%
Errors Corrected: 3
Avg Insert: 64.7
Standard Deviation: 11.7
Mode: 64
Insert range: 45 - 88
90th percentile: 77
75th percentile: 73
50th percentile: 64
25th percentile: 52
10th percentile: 45
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbmerge.sh -Xmx230g in1=./input/corrected/Edinburgh75_filtered_1.00.2_0.cor.fastq.gz in2=./input/corrected/Edinburgh75_filtered_2.00.2_0.cor.fastq.gz out=./input/Edinburgh75_ecco_PE.fastq ecco mix vstrict adapters=default
java -ea -Xmx230g -Xms230g -cp /DATA/markop/bbmap/current/ jgi.BBMerge -Xmx230g in1=./input/corrected/Edinburgh75_filtered_1.00.2_0.cor.fastq.gz in2=./input/corrected/Edinburgh75_filtered_2.00.2_0.cor.fastq.gz out=./input/Edinburgh75_ecco_PE.fastq ecco mix vstrict adapters=default
Executing jgi.BBMerge [-Xmx230g, in1=./input/corrected/Edinburgh75_filtered_1.00.2_0.cor.fastq.gz, in2=./input/corrected/Edinburgh75_filtered_2.00.2_0.cor.fastq.gz, out=./input/Edinburgh75_ecco_PE.fastq, ecco, mix, vstrict, adapters=default]
Version 38.34
Revised arguments: [maxbad=4, margin=3, minqo=8, qualiters=2, ratiomode=t, flatmode=f, minentropy=52, minoverlap=12, minoverlap0=4, maxratio=0.05, ratiomargin=12, ratiooffset=0.5, ratiominoverlapreduction=4, efilter=2, pfilter=0.008, minsecondratio=0.16, minapproxoverlap=22, in1=./input/corrected/Edinburgh75_filtered_1.00.2_0.cor.fastq.gz, in2=./input/corrected/Edinburgh75_filtered_2.00.2_0.cor.fastq.gz, out=./input/Edinburgh75_ecco_PE.fastq, ecco, mix, adapters=default]
Writing mergable reads interleaved.
Started output threads.
Total time: 1082.559 seconds.
Pairs: 198900577
Joined: 71356663 35.876%
Ambiguous: 127540144 64.123%
No Solution: 3770 0.002%
Too Short: 0 0.000%
Adapters Expected: 8293 0.002%
Adapters Found: 2366 0.001%
Errors Corrected: 616171
Avg Insert: 113.2
Standard Deviation: 15.7
Mode: 125
Insert range: 35 - 139
90th percentile: 132
75th percentile: 126
50th percentile: 115
25th percentile: 103
10th percentile: 92
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbmerge.sh -Xmx230g in=./input/corrected/Edinburgh75_filtered__unpaired.00.2_0.cor.fastq.gz out=./input/Edinburgh75_ecco_SE.fastq ecco mix vstrict adapters=default
java -ea -Xmx230g -Xms230g -cp /DATA/markop/bbmap/current/ jgi.BBMerge -Xmx230g in=./input/corrected/Edinburgh75_filtered__unpaired.00.2_0.cor.fastq.gz out=./input/Edinburgh75_ecco_SE.fastq ecco mix vstrict adapters=default
Executing jgi.BBMerge [-Xmx230g, in=./input/corrected/Edinburgh75_filtered__unpaired.00.2_0.cor.fastq.gz, out=./input/Edinburgh75_ecco_SE.fastq, ecco, mix, vstrict, adapters=default]
Version 38.34
Revised arguments: [maxbad=4, margin=3, minqo=8, qualiters=2, ratiomode=t, flatmode=f, minentropy=52, minoverlap=12, minoverlap0=4, maxratio=0.05, ratiomargin=12, ratiooffset=0.5, ratiominoverlapreduction=4, efilter=2, pfilter=0.008, minsecondratio=0.16, minapproxoverlap=22, in=./input/corrected/Edinburgh75_filtered__unpaired.00.2_0.cor.fastq.gz, out=./input/Edinburgh75_ecco_SE.fastq, ecco, mix, adapters=default]
Writing mergable reads interleaved.
Started output threads.
Total time: 4.751 seconds.
Pairs: 1627008
Joined: 16 0.001%
Ambiguous: 1626984 99.999%
No Solution: 8 0.000%
Too Short: 0 0.000%
Adapters Expected: 12 0.000%
Adapters Found: 0 0.000%
Errors Corrected: 1
Avg Insert: 103.1
Standard Deviation: 16.1
Mode: 84
Insert range: 75 - 126
90th percentile: 125
75th percentile: 113
50th percentile: 101
25th percentile: 84
10th percentile: 75
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $
Split time: 1.473 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13582756 reads: 4.665 seconds.
Making clumps.
Clump time: 0.617 seconds.
Correcting.
Correct time: 1.847 seconds.
Seed: 1
Reads: 13582756
Clumps: 372041
Corrections: 213846
Made a comparator with k=31, seed=2, border=0, hashes=4
Splitting.
Split time: 1.065 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13253038 reads: 138.990 seconds.
Making clumps.
Clump time: 0.942 seconds.
Correcting.
Correct time: 2.775 seconds.
Seed: 1
Reads: 13253038
Clumps: 371721
Corrections: 202658
Made a comparator with k=31, seed=2, border=0, hashes=4
Splitting.
Split time: 1.074 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13130857 reads: 0.000 seconds.
Making clumps.
Clump time: 0.561 seconds.
Correcting.
Correct time: 3.725 seconds.
Seed: 1
Reads: 13130857
Clumps: 370710
Corrections: 198039
Made a comparator with k=31, seed=2, border=0, hashes=4
Splitting.
Split time: 1.006 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 12810756 reads: 148.317 seconds.
Making clumps.
Clump time: 0.545 seconds.
Correcting.
Correct time: 2.194 seconds.
Seed: 1
Reads: 12810756
Clumps: 372008
Corrections: 195874
Made a comparator with k=31, seed=2, border=0, hashes=4
Splitting.
Split time: 1.777 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13344427 reads: 0.000 seconds.
Making clumps.
Clump time: 0.579 seconds.
Correcting.
Correct time: 2.474 seconds.
Seed: 1
Reads: 13344427
Clumps: 372386
Corrections: 201296
Made a comparator with k=31, seed=2, border=0, hashes=4
Splitting.
Split time: 1.016 seconds.
Writing.
Sent writable reads.
Fetching reads.
No more reads to fetch.
Adding poison.
Fetched 13444456 reads: 155.045 seconds.
Making clumps.
Clump time: 0.534 seconds.
Correcting.
Correct time: 2.404 seconds.
Seed: 1
Reads: 13444456
Clumps: 372679
Corrections: 205781
Made a comparator with k=31, seed=2, border=0, hashes=4
Splitting.
Split time: 1.587 seconds.
Writing.
Sent writable reads.
Fetching reads.
Encountered poison; count=1
A fetch thread finished.
No more reads to fetch.
Adding poison.
Fetched 13282704 reads: 3.134 seconds.
Making clumps.
Clump time: 0.596 seconds.
Correcting.
Correct time: 1.809 seconds.
Seed: 1
Reads: 13282704
Clumps: 370887
Corrections: 208181
Made a comparator with k=31, seed=2, border=0, hashes=4
Splitting.
Split time: 1.097 seconds.
Writing.
Sent writable reads.
Closing fetch threads.
A fetch thread finished.
Closed fetch threads.
Waiting for writing to complete.
Write time: 15.022 seconds.
Time: 971.598 seconds.
Reads Processed: 397m 409.43k reads/sec
Bases Processed: 29358m 30.22m bases/sec
Reads In: 397801154
Clumps Formed: 5577364
Errors Corrected: 3043143
Executing clump.KmerSort3 [in1=./input/Edinburgh75_eccc_PE_clumpify_p2_temp%_3c90d5d4353a9cc9.fastq, in2=, out=./input/Edinburgh75_eccc_PE_clumpify_p3_temp%_633a47e7bb4a8a87.fastq, out2=, groups=15, ecco=f, addname=false, shortname=f, unpair=f, repair=false, namesort=false, ow=true, ecc, passes=6]
Making comparator.
Made a comparator with k=31, seed=2, border=0, hashes=4
Making 2 fetch threads.
Starting threads.
Fetching reads.
Fetched 13091180 reads: 129.062 seconds.
Making clumps.
Clump time: 0.510 seconds.
Correcting.
Correct time: 1.605 seconds.
Seed: 2
Reads: 13091180
Clumps: 358703
Corrections: 71321
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 1.038 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13119819 reads: 0.000 seconds.
Making clumps.
Clump time: 0.392 seconds.
Correcting.
Correct time: 2.380 seconds.
Seed: 2
Reads: 13119819
Clumps: 358929
Corrections: 70737
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 0.902 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 12992765 reads: 139.304 seconds.
Making clumps.
Clump time: 0.361 seconds.
Correcting.
Correct time: 2.196 seconds.
Seed: 2
Reads: 12992765
Clumps: 358946
Corrections: 71299
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 1.037 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 12934479 reads: 0.000 seconds.
Making clumps.
Clump time: 0.419 seconds.
Correcting.
Correct time: 2.430 seconds.
Seed: 2
Reads: 12934479
Clumps: 357726
Corrections: 72451
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 0.905 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13088392 reads: 144.552 seconds.
Making clumps.
Clump time: 0.387 seconds.
Correcting.
Correct time: 2.003 seconds.
Seed: 2
Reads: 13088392
Clumps: 358241
Corrections: 72448
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 1.275 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13314848 reads: 1.664 seconds.
Making clumps.
Clump time: 0.429 seconds.
Correcting.
Correct time: 1.876 seconds.
Seed: 2
Reads: 13314848
Clumps: 357647
Corrections: 71829
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 0.928 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13361142 reads: 155.052 seconds.
Making clumps.
Clump time: 0.404 seconds.
Correcting.
Correct time: 2.070 seconds.
Seed: 2
Reads: 13361142
Clumps: 358597
Corrections: 70596
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 1.093 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13064664 reads: 0.000 seconds.
Making clumps.
Clump time: 0.446 seconds.
Correcting.
Correct time: 2.406 seconds.
Seed: 2
Reads: 13064664
Clumps: 359587
Corrections: 68348
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 0.936 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13480153 reads: 158.798 seconds.
Making clumps.
Clump time: 0.387 seconds.
Correcting.
Correct time: 1.987 seconds.
Seed: 2
Reads: 13480153
Clumps: 358583
Corrections: 72481
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 1.613 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13381331 reads: 3.395 seconds.
Making clumps.
Clump time: 0.440 seconds.
Correcting.
Correct time: 1.716 seconds.
Seed: 2
Reads: 13381331
Clumps: 358344
Corrections: 72828
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 1.139 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13227015 reads: 154.415 seconds.
Making clumps.
Clump time: 0.380 seconds.
Correcting.
Correct time: 1.702 seconds.
Seed: 2
Reads: 13227015
Clumps: 358387
Corrections: 68926
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 1.451 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13154705 reads: 4.745 seconds.
Making clumps.
Clump time: 0.359 seconds.
Correcting.
Correct time: 1.514 seconds.
Seed: 2
Reads: 13154705
Clumps: 359890
Corrections: 73568
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 1.243 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13281439 reads: 152.299 seconds.
Making clumps.
Clump time: 0.443 seconds.
Correcting.
Correct time: 1.987 seconds.
Seed: 2
Reads: 13281439
Clumps: 357759
Corrections: 73843
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 1.345 seconds.
Writing.
Sent writable reads.
Fetching reads.
No more reads to fetch.
Adding poison.
Fetched 13965547 reads: 3.242 seconds.
Making clumps.
Clump time: 0.373 seconds.
Correcting.
Correct time: 2.745 seconds.
Seed: 2
Reads: 13965547
Clumps: 357435
Corrections: 77075
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 1.229 seconds.
Writing.
Sent writable reads.
Fetching reads.
A fetch thread finished.
Encountered poison; count=1
No more reads to fetch.
Adding poison.
Fetched 13443098 reads: 112.889 seconds.
Making clumps.
Clump time: 0.342 seconds.
Correcting.
Correct time: 1.727 seconds.
Seed: 2
Reads: 13443098
Clumps: 358175
Corrections: 75716
Made a comparator with k=31, seed=3, border=0, hashes=4
Splitting.
Split time: 1.082 seconds.
Writing.
Sent writable reads.
Closing fetch threads.
A fetch thread finished.
Closed fetch threads.
Waiting for writing to complete.
Write time: 2.204 seconds.
Time: 1239.652 seconds.
Reads Processed: 397m 320.90k reads/sec
Bases Processed: 29358m 23.68m bases/sec
Reads In: 397801154
Clumps Formed: 5376949
Errors Corrected: 4126609
Executing clump.KmerSort3 [in1=./input/Edinburgh75_eccc_PE_clumpify_p3_temp%_633a47e7bb4a8a87.fastq, in2=, out=./input/Edinburgh75_eccc_PE_clumpify_p4_temp%_3edb2d95d2f22e59.fastq, out2=, groups=15, ecco=f, addname=false, shortname=f, unpair=f, repair=false, namesort=false, ow=true, ecc, passes=6]
Making comparator.
Made a comparator with k=31, seed=3, border=0, hashes=4
Making 2 fetch threads.
Starting threads.
Fetching reads.
Fetched 13266893 reads: 102.272 seconds.
Making clumps.
Clump time: 0.826 seconds.
Correcting.
Correct time: 1.990 seconds.
Seed: 3
Reads: 13266893
Clumps: 354554
Corrections: 35907
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 1.030 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13358539 reads: 0.000 seconds.
Making clumps.
Clump time: 0.391 seconds.
Correcting.
Correct time: 2.416 seconds.
Seed: 3
Reads: 13358539
Clumps: 355271
Corrections: 36904
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 1.087 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13476379 reads: 139.452 seconds.
Making clumps.
Clump time: 0.399 seconds.
Correcting.
Correct time: 2.306 seconds.
Seed: 3
Reads: 13476379
Clumps: 354923
Corrections: 36733
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 1.054 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13229294 reads: 0.000 seconds.
Making clumps.
Clump time: 0.517 seconds.
Correcting.
Correct time: 2.413 seconds.
Seed: 3
Reads: 13229294
Clumps: 354965
Corrections: 37245
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 0.946 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13186116 reads: 151.775 seconds.
Making clumps.
Clump time: 0.390 seconds.
Correcting.
Correct time: 1.971 seconds.
Seed: 3
Reads: 13186116
Clumps: 355423
Corrections: 39407
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 1.207 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13461725 reads: 0.000 seconds.
Making clumps.
Clump time: 0.439 seconds.
Correcting.
Correct time: 2.383 seconds.
Seed: 3
Reads: 13461725
Clumps: 353747
Corrections: 38012
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 24.959 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 12886206 reads: 131.126 seconds.
Making clumps.
Clump time: 0.354 seconds.
Correcting.
Correct time: 1.779 seconds.
Seed: 3
Reads: 12886206
Clumps: 354069
Corrections: 34898
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 1.111 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13761776 reads: 6.859 seconds.
Making clumps.
Clump time: 0.394 seconds.
Correcting.
Correct time: 1.959 seconds.
Seed: 3
Reads: 13761776
Clumps: 352696
Corrections: 36584
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 6.185 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13209716 reads: 149.606 seconds.
Making clumps.
Clump time: 0.375 seconds.
Correcting.
Correct time: 1.828 seconds.
Seed: 3
Reads: 13209716
Clumps: 354583
Corrections: 35063
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 1.274 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13026274 reads: 4.557 seconds.
Making clumps.
Clump time: 0.361 seconds.
Correcting.
Correct time: 2.168 seconds.
Seed: 3
Reads: 13026274
Clumps: 354094
Corrections: 36172
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 1.137 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 12878620 reads: 158.898 seconds.
Making clumps.
Clump time: 0.364 seconds.
Correcting.
Correct time: 1.810 seconds.
Seed: 3
Reads: 12878620
Clumps: 355017
Corrections: 36304
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 1.023 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13340482 reads: 13.602 seconds.
Making clumps.
Clump time: 0.349 seconds.
Correcting.
Correct time: 1.652 seconds.
Seed: 3
Reads: 13340482
Clumps: 355291
Corrections: 37192
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 0.937 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13624291 reads: 153.962 seconds.
Making clumps.
Clump time: 0.381 seconds.
Correcting.
Correct time: 1.693 seconds.
Seed: 3
Reads: 13624291
Clumps: 354169
Corrections: 38559
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 1.122 seconds.
Writing.
Sent writable reads.
Fetching reads.
No more reads to fetch.
Adding poison.
Fetched 13361996 reads: 5.118 seconds.
Making clumps.
Clump time: 0.337 seconds.
Correcting.
Correct time: 1.641 seconds.
Seed: 3
Reads: 13361996
Clumps: 354637
Corrections: 38260
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 0.966 seconds.
Writing.
Sent writable reads.
Fetching reads.
A fetch thread finished.
Encountered poison; count=1
No more reads to fetch.
Adding poison.
Fetched 12832270 reads: 121.822 seconds.
Making clumps.
Clump time: 0.325 seconds.
Correcting.
Correct time: 1.995 seconds.
Seed: 3
Reads: 12832270
Clumps: 353944
Corrections: 36669
Made a comparator with k=31, seed=4, border=0, hashes=4
Splitting.
Split time: 1.036 seconds.
Writing.
Sent writable reads.
Closing fetch threads.
A fetch thread finished.
Closed fetch threads.
Waiting for writing to complete.
Write time: 2.180 seconds.
Time: 1246.275 seconds.
Reads Processed: 397m 319.19k reads/sec
Bases Processed: 29358m 23.56m bases/sec
Reads In: 397801154
Clumps Formed: 5317383
Errors Corrected: 4680518
Executing clump.KmerSort3 [in1=./input/Edinburgh75_eccc_PE_clumpify_p4_temp%_3edb2d95d2f22e59.fastq, in2=, out=./input/Edinburgh75_eccc_PE_clumpify_p5_temp%_1d4e3de8ea94d25f.fastq, out2=, groups=15, ecco=f, addname=false, shortname=f, unpair=f, repair=false, namesort=false, ow=true, ecc, passes=6]
Making comparator.
Made a comparator with k=31, seed=4, border=0, hashes=4
Making 2 fetch threads.
Starting threads.
Fetching reads.
Fetched 12908021 reads: 107.499 seconds.
Making clumps.
Clump time: 0.767 seconds.
Correcting.
Correct time: 1.820 seconds.
Seed: 4
Reads: 12908021
Clumps: 352696
Corrections: 144647
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 1.219 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13339736 reads: 0.000 seconds.
Making clumps.
Clump time: 0.418 seconds.
Correcting.
Correct time: 2.587 seconds.
Seed: 4
Reads: 13339736
Clumps: 351988
Corrections: 145705
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 1.047 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13101797 reads: 143.415 seconds.
Making clumps.
Clump time: 0.379 seconds.
Correcting.
Correct time: 1.980 seconds.
Seed: 4
Reads: 13101797
Clumps: 352319
Corrections: 143556
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 1.485 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13609673 reads: 6.896 seconds.
Making clumps.
Clump time: 0.396 seconds.
Correcting.
Correct time: 1.756 seconds.
Seed: 4
Reads: 13609673
Clumps: 352680
Corrections: 146743
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 6.187 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13179639 reads: 143.183 seconds.
Making clumps.
Clump time: 0.371 seconds.
Correcting.
Correct time: 2.540 seconds.
Seed: 4
Reads: 13179639
Clumps: 351751
Corrections: 151862
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 1.510 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 12674107 reads: 4.606 seconds.
Making clumps.
Clump time: 0.344 seconds.
Correcting.
Correct time: 1.562 seconds.
Seed: 4
Reads: 12674107
Clumps: 351764
Corrections: 140333
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 1.005 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13287355 reads: 158.640 seconds.
Making clumps.
Clump time: 0.402 seconds.
Correcting.
Correct time: 1.779 seconds.
Seed: 4
Reads: 13287355
Clumps: 352078
Corrections: 147406
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 1.112 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13266547 reads: 7.866 seconds.
Making clumps.
Clump time: 0.366 seconds.
Correcting.
Correct time: 1.717 seconds.
Seed: 4
Reads: 13266547
Clumps: 352395
Corrections: 149987
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 1.101 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13311421 reads: 168.659 seconds.
Making clumps.
Clump time: 0.577 seconds.
Correcting.
Correct time: 1.929 seconds.
Seed: 4
Reads: 13311421
Clumps: 352605
Corrections: 143960
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 1.298 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13066372 reads: 0.000 seconds.
Making clumps.
Clump time: 0.548 seconds.
Correcting.
Correct time: 2.365 seconds.
Seed: 4
Reads: 13066372
Clumps: 352271
Corrections: 146525
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 1.058 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13283749 reads: 172.587 seconds.
Making clumps.
Clump time: 0.373 seconds.
Correcting.
Correct time: 1.644 seconds.
Seed: 4
Reads: 13283749
Clumps: 350940
Corrections: 148933
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 1.146 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13940611 reads: 9.958 seconds.
Making clumps.
Clump time: 0.359 seconds.
Correcting.
Correct time: 2.384 seconds.
Seed: 4
Reads: 13940611
Clumps: 352708
Corrections: 155542
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 6.620 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13269341 reads: 159.853 seconds.
Making clumps.
Clump time: 0.399 seconds.
Correcting.
Correct time: 1.834 seconds.
Seed: 4
Reads: 13269341
Clumps: 352406
Corrections: 148099
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 1.545 seconds.
Writing.
Sent writable reads.
Fetching reads.
No more reads to fetch.
Adding poison.
Fetched 13263146 reads: 4.610 seconds.
Making clumps.
Clump time: 0.382 seconds.
Correcting.
Correct time: 1.644 seconds.
Seed: 4
Reads: 13263146
Clumps: 351165
Corrections: 149244
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 1.253 seconds.
Writing.
Sent writable reads.
Fetching reads.
Encountered poison; count=1
A fetch thread finished.
No more reads to fetch.
Adding poison.
Fetched 13399062 reads: 128.520 seconds.
Making clumps.
Clump time: 0.360 seconds.
Correcting.
Correct time: 1.640 seconds.
Seed: 4
Reads: 13399062
Clumps: 350953
Corrections: 146735
Made a comparator with k=31, seed=5, border=0, hashes=4
Splitting.
Split time: 1.038 seconds.
Writing.
Sent writable reads.
Closing fetch threads.
A fetch thread finished.
Closed fetch threads.
Waiting for writing to complete.
Write time: 2.028 seconds.
Time: 1305.051 seconds.
Reads Processed: 397m 304.82k reads/sec
Bases Processed: 29358m 22.50m bases/sec
Reads In: 397801154
Clumps Formed: 5280719
Errors Corrected: 6889795
Executing clump.KmerSort3 [in1=./input/Edinburgh75_eccc_PE_clumpify_p5_temp%_1d4e3de8ea94d25f.fastq, in2=, out=./input/Edinburgh75_eccc_PE_clumpify_p6_temp%_6de24786a524afa0.fastq, out2=, groups=15, ecco=f, addname=false, shortname=f, unpair=f, repair=false, namesort=false, ow=true, ecc, passes=6]
Making comparator.
Made a comparator with k=31, seed=5, border=0, hashes=4
Making 2 fetch threads.
Starting threads.
Fetching reads.
Fetched 12657830 reads: 104.461 seconds.
Making clumps.
Clump time: 0.368 seconds.
Correcting.
Correct time: 3.674 seconds.
Seed: 5
Reads: 12657830
Clumps: 340521
Corrections: 49970
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 1.022 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 12996890 reads: 0.000 seconds.
Making clumps.
Clump time: 0.406 seconds.
Correcting.
Correct time: 2.379 seconds.
Seed: 5
Reads: 12996890
Clumps: 339522
Corrections: 50676
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 0.932 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13575035 reads: 157.075 seconds.
Making clumps.
Clump time: 0.396 seconds.
Correcting.
Correct time: 2.449 seconds.
Seed: 5
Reads: 13575035
Clumps: 339201
Corrections: 54975
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 1.497 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13209343 reads: 0.000 seconds.
Making clumps.
Clump time: 0.547 seconds.
Correcting.
Correct time: 2.470 seconds.
Seed: 5
Reads: 13209343
Clumps: 340150
Corrections: 50021
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 0.961 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13292584 reads: 166.203 seconds.
Making clumps.
Clump time: 0.678 seconds.
Correcting.
Correct time: 2.486 seconds.
Seed: 5
Reads: 13292584
Clumps: 340600
Corrections: 52463
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 1.071 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13460064 reads: 0.000 seconds.
Making clumps.
Clump time: 0.485 seconds.
Correcting.
Correct time: 2.506 seconds.
Seed: 5
Reads: 13460064
Clumps: 340363
Corrections: 54713
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 1.098 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13075002 reads: 173.184 seconds.
Making clumps.
Clump time: 0.358 seconds.
Correcting.
Correct time: 2.291 seconds.
Seed: 5
Reads: 13075002
Clumps: 340097
Corrections: 50919
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 1.475 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13571328 reads: 2.791 seconds.
Making clumps.
Clump time: 0.376 seconds.
Correcting.
Correct time: 1.948 seconds.
Seed: 5
Reads: 13571328
Clumps: 340854
Corrections: 54444
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 6.551 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13150319 reads: 170.310 seconds.
Making clumps.
Clump time: 0.361 seconds.
Correcting.
Correct time: 1.918 seconds.
Seed: 5
Reads: 13150319
Clumps: 340414
Corrections: 52545
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 1.565 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 12894462 reads: 2.750 seconds.
Making clumps.
Clump time: 0.360 seconds.
Correcting.
Correct time: 1.611 seconds.
Seed: 5
Reads: 12894462
Clumps: 339738
Corrections: 50892
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 1.075 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13316006 reads: 183.449 seconds.
Making clumps.
Clump time: 0.446 seconds.
Correcting.
Correct time: 2.545 seconds.
Seed: 5
Reads: 13316006
Clumps: 339969
Corrections: 53477
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 1.191 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13391897 reads: 0.000 seconds.
Making clumps.
Clump time: 0.417 seconds.
Correcting.
Correct time: 2.571 seconds.
Seed: 5
Reads: 13391897
Clumps: 340476
Corrections: 50805
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 3.606 seconds.
Writing.
Sent writable reads.
Fetching reads.
Fetched 13606644 reads: 171.811 seconds.
Making clumps.
Clump time: 0.370 seconds.
Correcting.
Correct time: 2.176 seconds.
Seed: 5
Reads: 13606644
Clumps: 339032
Corrections: 52432
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 1.227 seconds.
Writing.
Sent writable reads.
Fetching reads.
No more reads to fetch.
Adding poison.
Fetched 13362745 reads: 6.161 seconds.
Making clumps.
Clump time: 0.362 seconds.
Correcting.
Correct time: 1.793 seconds.
Seed: 5
Reads: 13362745
Clumps: 340320
Corrections: 53027
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 6.361 seconds.
Writing.
Sent writable reads.
Fetching reads.
Encountered poison; count=1
A fetch thread finished.
No more reads to fetch.
Adding poison.
Fetched 13340428 reads: 133.387 seconds.
Making clumps.
Clump time: 0.366 seconds.
Correcting.
Correct time: 1.855 seconds.
Seed: 5
Reads: 13340428
Clumps: 341238
Corrections: 52846
Made a comparator with k=31, seed=6, border=0, hashes=4
Splitting.
Split time: 1.037 seconds.
Writing.
Sent writable reads.
Closing fetch threads.
A fetch thread finished.
Closed fetch threads.
Waiting for writing to complete.
Write time: 1.994 seconds.
Time: 1368.887 seconds.
Reads Processed: 397m 290.60k reads/sec
Bases Processed: 29358m 21.45m bases/sec
Reads In: 397801154
Clumps Formed: 5102495
Errors Corrected: 7674000
Executing clump.KmerSort3 [in1=./input/Edinburgh75_eccc_PE_clumpify_p6_temp%_6de24786a524afa0.fastq, in2=, out=./input/Edinburgh75_eccc_PE.fastq, out2=, groups=15, ecco=f, addname=false, shortname=f, unpair=f, repair=false, namesort=false, ow=true, ecc, passes=6]
Making comparator.
Made a comparator with k=31, seed=6, border=0, hashes=4
Making 2 fetch threads.
Starting threads.
Fetching reads.
Fetched 13018466 reads: 110.766 seconds.
Making clumps.
Clump time: 0.458 seconds.
Correcting.
Correct time: 2.709 seconds.
Seed: 6
Reads: 13018466
Clumps: 333657
Corrections: 26820
Writing.
Fetching reads.
Fetched 13128606 reads: 0.000 seconds.
Making clumps.
Clump time: 0.361 seconds.
Correcting.
Correct time: 1.933 seconds.
Seed: 6
Reads: 13128606
Clumps: 334379
Corrections: 25072
Writing.
Fetching reads.
Fetched 13148859 reads: 163.027 seconds.
Making clumps.
Clump time: 0.398 seconds.
Correcting.
Correct time: 2.502 seconds.
Seed: 6
Reads: 13148859
Clumps: 334540
Corrections: 25705
Writing.
Fetching reads.
Fetched 13100261 reads: 0.000 seconds.
Making clumps.
Clump time: 0.334 seconds.
Correcting.
Correct time: 1.777 seconds.
Seed: 6
Reads: 13100261
Clumps: 334068
Corrections: 25217
Writing.
Fetching reads.
Fetched 13573439 reads: 177.294 seconds.
Making clumps.
Clump time: 0.730 seconds.
Correcting.
Correct time: 2.322 seconds.
Seed: 6
Reads: 13573439
Clumps: 333814
Corrections: 29745
Writing.
Fetching reads.
Fetched 13061500 reads: 0.000 seconds.
Making clumps.
Clump time: 0.372 seconds.
Correcting.
Correct time: 1.903 seconds.
Seed: 6
Reads: 13061500
Clumps: 333970
Corrections: 27682
Writing.
Fetching reads.
Fetched 13199144 reads: 185.552 seconds.
Making clumps.
Clump time: 0.392 seconds.
Correcting.
Correct time: 2.361 seconds.
Seed: 6
Reads: 13199144
Clumps: 334778
Corrections: 26163
Writing.
Fetching reads.
Fetched 13658367 reads: 2.032 seconds.
Making clumps.
Clump time: 0.373 seconds.
Correcting.
Correct time: 1.766 seconds.
Seed: 6
Reads: 13658367
Clumps: 334685
Corrections: 29337
Writing.
Fetching reads.
Fetched 13464957 reads: 188.354 seconds.
Making clumps.
Clump time: 0.357 seconds.
Correcting.
Correct time: 1.997 seconds.
Seed: 6
Reads: 13464957
Clumps: 333773
Corrections: 27275
Writing.
Fetching reads.
Fetched 13293233 reads: 4.876 seconds.
Making clumps.
Clump time: 0.353 seconds.
Correcting.
Correct time: 1.782 seconds.
Seed: 6
Reads: 13293233
Clumps: 333820
Corrections: 25819
Writing.
Fetching reads.
Fetched 13650432 reads: 186.349 seconds.
Making clumps.
Clump time: 0.459 seconds.
Correcting.
Correct time: 2.891 seconds.
Seed: 6
Reads: 13650432
Clumps: 333355
Corrections: 27159
Writing.
Fetching reads.
Fetched 13045723 reads: 0.000 seconds.
Making clumps.
Clump time: 0.377 seconds.
Correcting.
Correct time: 1.799 seconds.
Seed: 6
Reads: 13045723
Clumps: 334100
Corrections: 27195
Writing.
Fetching reads.
Fetched 12594195 reads: 195.588 seconds.
Making clumps.
Clump time: 0.424 seconds.
Correcting.
Correct time: 3.392 seconds.
Seed: 6
Reads: 12594195
Clumps: 334347
Corrections: 24327
Writing.
Fetching reads.
No more reads to fetch.
Adding poison.
Fetched 13708864 reads: 0.000 seconds.
Making clumps.
Clump time: 0.392 seconds.
Correcting.
Correct time: 2.105 seconds.
Seed: 6
Reads: 13708864
Clumps: 333907
Corrections: 27962
Writing.
Fetching reads.
Encountered poison; count=1
A fetch thread finished.
No more reads to fetch.
Adding poison.
Fetched 13254531 reads: 143.106 seconds.
Making clumps.
Clump time: 0.349 seconds.
Correcting.
Correct time: 1.746 seconds.
Seed: 6
Reads: 13254531
Clumps: 332372
Corrections: 27151
Writing.
Closing fetch threads.
A fetch thread finished.
Closed fetch threads.
Waiting for writing to complete.
Write time: 17.502 seconds.
Done!
Time: 1434.846 seconds.
Reads Processed: 397m 277.24k reads/sec
Bases Processed: 29358m 20.46m bases/sec
Reads In: 397801154
Clumps Formed: 5009565
Errors Corrected: 8076629
Total time: 8694.633 seconds.
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/clumpify.sh -Xmx200g in=./input/Edinburgh75_ecco_SE.fastq out=./input/Edinburgh75_eccc_SE.fastq ecc passes=6 minid=0.98
java -ea -Xmx200g -Xms200g -cp /DATA/markop/bbmap/current/ clump.Clumpify -Xmx200g in=./input/Edinburgh75_ecco_SE.fastq out=./input/Edinburgh75_eccc_SE.fastq ecc passes=6 minid=0.98
Executing clump.Clumpify [-Xmx200g, in=./input/Edinburgh75_ecco_SE.fastq, out=./input/Edinburgh75_eccc_SE.fastq, ecc, passes=6, minid=0.98]
Version 38.34
Read Estimate: 6962194
Memory Estimate: 5311 MB
Memory Available: 160900 MB
Set groups to 1
Executing clump.KmerSort1 [in1=./input/Edinburgh75_ecco_SE.fastq, in2=, out1=./input/Edinburgh75_eccc_SE.fastq, out2=, groups=1, ecco=false, rename=false, shortname=f, unpair=false, repair=false, namesort=false, ow=true, ecc, passes=6]
Making comparator.
Made a comparator with k=31, seed=1, border=1, hashes=4
Starting cris 0.
Fetching reads.
Making fetch threads.
Starting threads.
Waiting for threads.
Fetch time: 6.804 seconds.
Closing input stream.
Combining thread output.
Combine time: 0.038 seconds.
Sorting.
Sort time: 1.040 seconds.
Making clumps.
Clump time: 0.707 seconds.
Correcting.
Correct time: 1.376 seconds.
Seed: 1
Pass 1.
Reads: 3254016
Clumps: 1010148
Corrections: 26784
Made a comparator with k=31, seed=2, border=0, hashes=4
Hashing.
Hash time: 0.477 seconds.
Sorting.
Sort time: 0.627 seconds.
Making clumps.
Clump time: 0.178 seconds.
Correcting.
Correct time: 0.519 seconds.
Seed: 2
Pass 2.
Reads: 3254016
Clumps: 987055
Corrections: 11505
Made a comparator with k=31, seed=3, border=0, hashes=4
Hashing.
Hash time: 0.338 seconds.
Sorting.
Sort time: 0.497 seconds.
Making clumps.
Clump time: 0.144 seconds.
Correcting.
Correct time: 0.386 seconds.
Seed: 3
Pass 3.
Reads: 3254016
Clumps: 985175
Corrections: 6456
Made a comparator with k=31, seed=4, border=0, hashes=4
Hashing.
Hash time: 0.269 seconds.
Sorting.
Sort time: 0.490 seconds.
Making clumps.
Clump time: 0.139 seconds.
Correcting.
Correct time: 0.420 seconds.
Seed: 4
Pass 4.
Reads: 3254016
Clumps: 983817
Corrections: 26754
Made a comparator with k=31, seed=5, border=0, hashes=4
Hashing.
Hash time: 0.277 seconds.
Sorting.
Sort time: 0.479 seconds.
Making clumps.
Clump time: 0.150 seconds.
Correcting.
Correct time: 0.417 seconds.
Seed: 5
Pass 5.
Reads: 3254016
Clumps: 977792
Corrections: 12622
Made a comparator with k=31, seed=6, border=0, hashes=4
Hashing.
Hash time: 0.254 seconds.
Sorting.
Sort time: 0.471 seconds.
Making clumps.
Clump time: 0.132 seconds.
Correcting.
Correct time: 0.403 seconds.
Seed: 6
Pass 6.
Reads: 3254016
Clumps: 974804
Corrections: 7721
Writing.
Waiting for writing to complete.
Write time: 3.184 seconds.
Done!
Time: 20.372 seconds.
Reads Processed: 3254k 159.73k reads/sec
Bases Processed: 226m 11.11m bases/sec
Reads In: 3254016
Clumps Formed: 974804
Errors Corrected: 91842
Total time: 21.472 seconds.
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ #Error-correct 3
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/tadpole.sh -Xmx200g in=./input/SUSPHIRE_eccc_PE.fastq out=./input/SUSPHIRE_ecct_PE.fastq ecc
java -ea -Xmx200g -Xms200g -cp /DATA/markop/bbmap/current/ assemble.Tadpole -Xmx200g in=./input/SUSPHIRE_eccc_PE.fastq out=./input/SUSPHIRE_ecct_PE.fastq ecc
Executing assemble.Tadpole1 [-Xmx200g, in=./input/SUSPHIRE_eccc_PE.fastq, out=./input/SUSPHIRE_ecct_PE.fastq, ecc]
Version 38.34
Switching to correct mode because ecc=t.
Using 32 threads.
Executing kmer.KmerTableSet [-Xmx200g, in=./input/SUSPHIRE_eccc_PE.fastq, out=./input/SUSPHIRE_ecct_PE.fastq, ecc]
Initial:
Ways=83, initialSize=128000, prefilter=f, prealloc=f
Memory: max=205800m, total=205800m, free=201505m, used=4295m
Initialization Time: 0.106 seconds.
Loading kmers.
Estimated kmer capacity: 9967382606
0.106 seconds.
After table allocation:
Memory: max=205800m, total=205800m, free=199358m, used=6442m
After loading:
Memory: max=202321m, total=202321m, free=171393m, used=30928m
Input: 657590806 reads 91484444833 bases.
Unique Kmers: 552172950
Load Time: 1663.494 seconds.
Reads Processed: 657m 395.31k reads/sec
Bases Processed: 91484m 55.00m bases/sec
Extending/error-correcting/discarding.
After extending reads:
Memory: max=207874m, total=207874m, free=158381m, used=49493m
Input: 657590806 reads 91484444833 bases.
Output: 657590806 reads 91484444833 bases.
Errors detected: 196974975
Errors corrected: 47494332 (47494332 reassemble)
Reads with errors detected: 51850915 (7.88%)
Reads fully corrected: 39562025 (76.30% of detected)
Reads partly corrected: 954140 (1.84% of detected)
Rollbacks: 1296461 (2.50% of detected)
Extend/error-correct time: 3656.093 seconds.
Total Time: 5319.712 seconds.
Reads Processed: 657m 123.61k reads/sec
Bases Processed: 91484m 17.20m bases/sec
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/tadpole.sh -Xmx200g in=./input/SUSPHIRE_eccc_SE.fastq out=./input/SUSPHIRE_ecct_SE.fastq ecc
java -ea -Xmx200g -Xms200g -cp /DATA/markop/bbmap/current/ assemble.Tadpole -Xmx200g in=./input/SUSPHIRE_eccc_SE.fastq out=./input/SUSPHIRE_ecct_SE.fastq ecc
Executing assemble.Tadpole1 [-Xmx200g, in=./input/SUSPHIRE_eccc_SE.fastq, out=./input/SUSPHIRE_ecct_SE.fastq, ecc]
Version 38.34
Switching to correct mode because ecc=t.
Using 32 threads.
Executing kmer.KmerTableSet [-Xmx200g, in=./input/SUSPHIRE_eccc_SE.fastq, out=./input/SUSPHIRE_ecct_SE.fastq, ecc]
Initial:
Ways=83, initialSize=128000, prefilter=f, prealloc=f
Memory: max=205800m, total=205800m, free=201505m, used=4295m
Initialization Time: 0.108 seconds.
Loading kmers.
Estimated kmer capacity: 9967382606
0.100 seconds.
After table allocation:
Memory: max=205800m, total=205800m, free=199358m, used=6442m
After loading:
Memory: max=205800m, total=205800m, free=160703m, used=45097m
Input: 2837572 reads 328381653 bases.
Unique Kmers: 40402852
Load Time: 6.577 seconds.
Reads Processed: 2837k 431.42k reads/sec
Bases Processed: 328m 49.93m bases/sec
Extending/error-correcting/discarding.
After extending reads:
Memory: max=205800m, total=205800m, free=186062m, used=19738m
Input: 2837572 reads 328381653 bases.
Output: 2837572 reads 328381653 bases.
Errors detected: 881943
Errors corrected: 241196 (241196 reassemble)
Reads with errors detected: 221954 (7.82%)
Reads fully corrected: 163196 (73.53% of detected)
Reads partly corrected: 8445 (3.80% of detected)
Rollbacks: 4390 (1.98% of detected)
Extend/error-correct time: 5.241 seconds.
Total Time: 11.942 seconds.
Reads Processed: 2837k 237.62k reads/sec
Bases Processed: 328m 27.50m bases/sec
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/tadpole.sh -Xmx200g in=./input/Edinburgh50_eccc_PE.fastq out=./input/Edinburgh50_ecct_PE.fastq ecc
java -ea -Xmx200g -Xms200g -cp /DATA/markop/bbmap/current/ assemble.Tadpole -Xmx200g in=./input/Edinburgh50_eccc_PE.fastq out=./input/Edinburgh50_ecct_PE.fastq ecc
Executing assemble.Tadpole1 [-Xmx200g, in=./input/Edinburgh50_eccc_PE.fastq, out=./input/Edinburgh50_ecct_PE.fastq, ecc]
Version 38.34
Switching to correct mode because ecc=t.
Using 32 threads.
Executing kmer.KmerTableSet [-Xmx200g, in=./input/Edinburgh50_eccc_PE.fastq, out=./input/Edinburgh50_ecct_PE.fastq, ecc]
Initial:
Ways=83, initialSize=128000, prefilter=f, prealloc=f
Memory: max=205800m, total=205800m, free=200432m, used=5368m
Initialization Time: 0.051 seconds.
Loading kmers.
Estimated kmer capacity: 9967382606
0.075 seconds.
After table allocation:
Memory: max=205800m, total=205800m, free=198284m, used=7516m
After loading:
Memory: max=205800m, total=205800m, free=156139m, used=49661m
Input: 283588028 reads 13727921131 bases.
Unique Kmers: 125298285
Load Time: 279.276 seconds.
Reads Processed: 283m 1015.44k reads/sec
Bases Processed: 13727m 49.16m bases/sec
Extending/error-correcting/discarding.
After extending reads:
Memory: max=210014m, total=210014m, free=196488m, used=13526m
Input: 283588028 reads 13727921131 bases.
Output: 283588028 reads 13727921131 bases.
Errors detected: 23182982
Errors corrected: 9704110 (9704110 reassemble)
Reads with errors detected: 10259616 (3.62%)
Reads fully corrected: 8640642 (84.22% of detected)
Reads partly corrected: 22311 (0.22% of detected)
Rollbacks: 185096 (1.80% of detected)
Extend/error-correct time: 236.059 seconds.
Total Time: 515.401 seconds.
Reads Processed: 283m 550.23k reads/sec
Bases Processed: 13727m 26.64m bases/sec
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/tadpole.sh -Xmx200g in=./input/Edinburgh50_eccc_SE.fastq out=./input/Edinburgh50_ecct_SE.fastq ecc
java -ea -Xmx200g -Xms200g -cp /DATA/markop/bbmap/current/ assemble.Tadpole -Xmx200g in=./input/Edinburgh50_eccc_SE.fastq out=./input/Edinburgh50_ecct_SE.fastq ecc
Executing assemble.Tadpole1 [-Xmx200g, in=./input/Edinburgh50_eccc_SE.fastq, out=./input/Edinburgh50_ecct_SE.fastq, ecc]
Version 38.34
Switching to correct mode because ecc=t.
Using 32 threads.
Executing kmer.KmerTableSet [-Xmx200g, in=./input/Edinburgh50_eccc_SE.fastq, out=./input/Edinburgh50_ecct_SE.fastq, ecc]
Initial:
Ways=83, initialSize=128000, prefilter=f, prealloc=f
Memory: max=205800m, total=205800m, free=201505m, used=4295m
Initialization Time: 0.046 seconds.
Loading kmers.
Estimated kmer capacity: 9967382606
0.080 seconds.
After table allocation:
Memory: max=205800m, total=205800m, free=199358m, used=6442m
After loading:
Memory: max=205800m, total=205800m, free=154260m, used=51540m
Input: 11623998 reads 542614828 bases.
Unique Kmers: 30621138
Load Time: 66.883 seconds.
Reads Processed: 11623k 173.80k reads/sec
Bases Processed: 542m 8.11m bases/sec
Extending/error-correcting/discarding.
After extending reads:
Memory: max=205800m, total=205800m, free=182303m, used=23497m
Input: 11623998 reads 542614828 bases.
Output: 11623998 reads 542614828 bases.
Errors detected: 619167
Errors corrected: 414397 (414397 reassemble)
Reads with errors detected: 404384 (3.48%)
Reads fully corrected: 373967 (92.48% of detected)
Reads partly corrected: 631 (0.16% of detected)
Rollbacks: 3222 (0.80% of detected)
Extend/error-correct time: 11.981 seconds.
Total Time: 78.924 seconds.
Reads Processed: 11623k 147.28k reads/sec
Bases Processed: 542m 6.88m bases/sec
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/tadpole.sh -Xmx200g in=./input/Edinburgh75_eccc_PE.fastq out=./input/Edinburgh75_ecct_PE.fastq ecc
java -ea -Xmx200g -Xms200g -cp /DATA/markop/bbmap/current/ assemble.Tadpole -Xmx200g in=./input/Edinburgh75_eccc_PE.fastq out=./input/Edinburgh75_ecct_PE.fastq ecc
Executing assemble.Tadpole1 [-Xmx200g, in=./input/Edinburgh75_eccc_PE.fastq, out=./input/Edinburgh75_ecct_PE.fastq, ecc]
Version 38.34
Switching to correct mode because ecc=t.
Using 32 threads.
Executing kmer.KmerTableSet [-Xmx200g, in=./input/Edinburgh75_eccc_PE.fastq, out=./input/Edinburgh75_ecct_PE.fastq, ecc]
Initial:
Ways=83, initialSize=128000, prefilter=f, prealloc=f
Memory: max=205800m, total=205800m, free=200432m, used=5368m
Initialization Time: 0.047 seconds.
Loading kmers.
Estimated kmer capacity: 9967382606
0.091 seconds.
After table allocation:
Memory: max=205800m, total=205800m, free=197210m, used=8590m
After loading:
Memory: max=209633m, total=209633m, free=157558m, used=52075m
Input: 397801154 reads 29358174269 bases.
Unique Kmers: 227287476
Load Time: 663.791 seconds.
Reads Processed: 397m 599.29k reads/sec
Bases Processed: 29358m 44.23m bases/sec
Extending/error-correcting/discarding.
After extending reads:
Memory: max=203106m, total=203106m, free=164776m, used=38330m
Input: 397801154 reads 29358174269 bases.
Output: 397801154 reads 29358174269 bases.
Errors detected: 38353861
Errors corrected: 10940201 (10940201 reassemble)
Reads with errors detected: 11985095 (3.01%)
Reads fully corrected: 9172227 (76.53% of detected)
Reads partly corrected: 96796 (0.81% of detected)
Rollbacks: 232142 (1.94% of detected)
Extend/error-correct time: 1177.362 seconds.
Total Time: 1841.214 seconds.
Reads Processed: 397m 216.05k reads/sec
Bases Processed: 29358m 15.95m bases/sec
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/tadpole.sh -Xmx200g in=./input/Edinburgh75_eccc_SE.fastq out=./input/Edinburgh75_ecct_SE.fastq ecc
java -ea -Xmx200g -Xms200g -cp /DATA/markop/bbmap/current/ assemble.Tadpole -Xmx200g in=./input/Edinburgh75_eccc_SE.fastq out=./input/Edinburgh75_ecct_SE.fastq ecc
Executing assemble.Tadpole1 [-Xmx200g, in=./input/Edinburgh75_eccc_SE.fastq, out=./input/Edinburgh75_ecct_SE.fastq, ecc]
Version 38.34
Switching to correct mode because ecc=t.
Using 32 threads.
Executing kmer.KmerTableSet [-Xmx200g, in=./input/Edinburgh75_eccc_SE.fastq, out=./input/Edinburgh75_ecct_SE.fastq, ecc]
Initial:
Ways=83, initialSize=128000, prefilter=f, prealloc=f
Memory: max=205800m, total=205800m, free=201505m, used=4295m
Initialization Time: 0.156 seconds.
Loading kmers.
Estimated kmer capacity: 9967382606
0.103 seconds.
After table allocation:
Memory: max=205800m, total=205800m, free=199358m, used=6442m
After loading:
Memory: max=205800m, total=205800m, free=158555m, used=47245m
Input: 3254016 reads 226333557 bases.
Unique Kmers: 26141855
Load Time: 5.658 seconds.
Reads Processed: 3254k 575.09k reads/sec
Bases Processed: 226m 40.00m bases/sec
Extending/error-correcting/discarding.
After extending reads:
Memory: max=205800m, total=205800m, free=183147m, used=22653m
Input: 3254016 reads 226333557 bases.
Output: 3254016 reads 226333557 bases.
Errors detected: 288535
Errors corrected: 90792 (90792 reassemble)
Reads with errors detected: 99801 (3.07%)
Reads fully corrected: 74167 (74.31% of detected)
Reads partly corrected: 1595 (1.60% of detected)
Rollbacks: 989 (0.99% of detected)
Extend/error-correct time: 4.550 seconds.
Total Time: 10.384 seconds.
Reads Processed: 3254k 313.36k reads/sec
Bases Processed: 226m 21.80m bases/sec
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ #Merge
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbmerge.sh -Xmx200g in=./input/SUSPHIRE_ecct_PE.fastq out=./input/SUSPHIRE_merged.fastq outu=./input/SUSPHIRE_unmerged.fastq rem k=62 extend2=50 adapters=default
java -ea -Xmx200g -Xms200g -cp /DATA/markop/bbmap/current/ jgi.BBMerge -Xmx200g in=./input/SUSPHIRE_ecct_PE.fastq out=./input/SUSPHIRE_merged.fastq outu=./input/SUSPHIRE_unmerged.fastq rem k=62 extend2=50 adapters=default
Executing jgi.BBMerge [-Xmx200g, in=./input/SUSPHIRE_ecct_PE.fastq, out=./input/SUSPHIRE_merged.fastq, outu=./input/SUSPHIRE_unmerged.fastq, rem, k=62, extend2=50, adapters=default]
Version 38.34
Executing assemble.Tadpole2 [in=./input/SUSPHIRE_ecct_PE.fastq, branchlower=3, branchmult1=20.0, branchmult2=3.0, mincountseed=3, mincountextend=2, minprob=0.5, k=62, prealloc=false, prefilter=0, ecctail=false, eccpincer=false, eccreassemble=true]
Version 38.34
Using 32 threads.
Executing ukmer.KmerTableSetU [in=./input/SUSPHIRE_ecct_PE.fastq, branchlower=3, branchmult1=20.0, branchmult2=3.0, mincountseed=3, mincountextend=2, minprob=0.5, k=62, prealloc=false, prefilter=0, ecctail=false, eccpincer=false, eccreassemble=true]
Initial:
Ways=83, initialSize=128000, prefilter=f, prealloc=f
Memory: max=205800m, total=205800m, free=201505m, used=4295m
Estimated kmer capacity: 4784343650
After table allocation:
Memory: max=205800m, total=205800m, free=198284m, used=7516m
/DATA/markop/bbmap/bbmerge.sh -Xmx200g in=./input/Edinburgh50_ecct_PE.fastq out=./input/Edinburgh50_merged.fastq outu=./input/Edinburgh50_unmerged.fastq rem k=62 extend2=50 adapters=default
/DATA/markop/bbmap/bbmerge.sh -Xmx200g in=./input/Edinburgh75_ecct_PE.fastq out=./input/Edinburgh75_merged.fastq outu=./input/Edinburgh75_unmerged.fastq rem k=62 extend2=50 adapters=default
After loading:
Memory: max=199649m, total=199649m, free=173936m, used=25713m
Input: 657590806 reads 91484444833 bases.
Unique Kmers: 484281517
Load Time: 1745.330 seconds.
Writing mergable reads merged.
Started output threads.
Total time: 5607.393 seconds.
Pairs: 328795403
Joined: 281041277 85.476%
Ambiguous: 47255788 14.372%
No Solution: 498338 0.152%
Too Short: 0 0.000%
Fully Extended: 582053062 88.518%
Partly Extended: 51108156 7.773%
Not Extended: 24389436 3.709%
Adapters Expected: 457268 0.070%
Adapters Found: 93372 0.014%
Avg Insert: 207.1
Standard Deviation: 69.9
Mode: 167
Insert range: 35 - 391
90th percentile: 310
75th percentile: 254
50th percentile: 197
25th percentile: 153
10th percentile: 123
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbmerge.sh -Xmx200g in=./input/Edinburgh50_ecct_PE.fastq out=./input/Edinburgh50_merged.fastq outu=./input/Edinburgh50_unmerged.fastq rem k=62 extend2=50 adapters=default
java -ea -Xmx200g -Xms200g -cp /DATA/markop/bbmap/current/ jgi.BBMerge -Xmx200g in=./input/Edinburgh50_ecct_PE.fastq out=./input/Edinburgh50_merged.fastq outu=./input/Edinburgh50_unmerged.fastq rem k=62 extend2=50 adapters=default
Executing jgi.BBMerge [-Xmx200g, in=./input/Edinburgh50_ecct_PE.fastq, out=./input/Edinburgh50_merged.fastq, outu=./input/Edinburgh50_unmerged.fastq, rem, k=62, extend2=50, adapters=default]
Version 38.34
Executing assemble.Tadpole2 [in=./input/Edinburgh50_ecct_PE.fastq, branchlower=3, branchmult1=20.0, branchmult2=3.0, mincountseed=3, mincountextend=2, minprob=0.5, k=62, prealloc=false, prefilter=0, ecctail=false, eccpincer=false, eccreassemble=true]
Version 38.34
Using 32 threads.
Executing ukmer.KmerTableSetU [in=./input/Edinburgh50_ecct_PE.fastq, branchlower=3, branchmult1=20.0, branchmult2=3.0, mincountseed=3, mincountextend=2, minprob=0.5, k=62, prealloc=false, prefilter=0, ecctail=false, eccpincer=false, eccreassemble=true]
Initial:
Ways=83, initialSize=128000, prefilter=f, prealloc=f
Memory: max=205800m, total=205800m, free=201505m, used=4295m
Estimated kmer capacity: 4784343650
After table allocation:
Memory: max=205800m, total=205800m, free=198284m, used=7516m
After loading:
Memory: max=205800m, total=205800m, free=157987m, used=47813m
Input: 283588028 reads 13727921131 bases.
Unique Kmers: 0
Load Time: 266.192 seconds.
Writing mergable reads merged.
Started output threads.
Total time: 549.072 seconds.
Pairs: 141794014
Joined: 1848856 1.304%
Ambiguous: 139941580 98.694%
No Solution: 3578 0.003%
Too Short: 0 0.000%
Fully Extended: 0 0.000%
Partly Extended: 0 0.000%
Not Extended: 283580982 100.000%
Adapters Expected: 7265 0.003%
Adapters Found: 861 0.000%
Avg Insert: 80.5
Standard Deviation: 9.1
Mode: 89
Insert range: 35 - 91
90th percentile: 89
75th percentile: 87
50th percentile: 83
25th percentile: 77
10th percentile: 68
administrator@bufo /DATA/markop/Pcitri_rnaspades_alldata $ /DATA/markop/bbmap/bbmerge.sh -Xmx200g in=./input/Edinburgh75_ecct_PE.fastq out=./input/Edinburgh75_merged.fastq outu=./input/Edinburgh75_unmerged.fastq rem k=62 extend2=50 adapters=default
java -ea -Xmx200g -Xms200g -cp /DATA/markop/bbmap/current/ jgi.BBMerge -Xmx200g in=./input/Edinburgh75_ecct_PE.fastq out=./input/Edinburgh75_merged.fastq outu=./input/Edinburgh75_unmerged.fastq rem k=62 extend2=50 adapters=default
Executing jgi.BBMerge [-Xmx200g, in=./input/Edinburgh75_ecct_PE.fastq, out=./input/Edinburgh75_merged.fastq, outu=./input/Edinburgh75_unmerged.fastq, rem, k=62, extend2=50, adapters=default]
Version 38.34
Executing assemble.Tadpole2 [in=./input/Edinburgh75_ecct_PE.fastq, branchlower=3, branchmult1=20.0, branchmult2=3.0, mincountseed=3, mincountextend=2, minprob=0.5, k=62, prealloc=false, prefilter=0, ecctail=false, eccpincer=false, eccreassemble=true]
Version 38.34
Using 32 threads.
Executing ukmer.KmerTableSetU [in=./input/Edinburgh75_ecct_PE.fastq, branchlower=3, branchmult1=20.0, branchmult2=3.0, mincountseed=3, mincountextend=2, minprob=0.5, k=62, prealloc=false, prefilter=0, ecctail=false, eccpincer=false, eccreassemble=true]
Initial:
Ways=83, initialSize=128000, prefilter=f, prealloc=f
Memory: max=205800m, total=205800m, free=201505m, used=4295m
Estimated kmer capacity: 4784343650
After table allocation:
Memory: max=205800m, total=205800m, free=199358m, used=6442m
After loading:
Memory: max=210619m, total=210619m, free=161622m, used=48997m
Input: 397801154 reads 29358174269 bases.
Unique Kmers: 110012150
Load Time: 588.107 seconds.
Writing mergable reads merged.
Started output threads.
Total time: 2135.634 seconds.
Pairs: 198900577
Joined: 167017503 83.970%
Ambiguous: 31436521 15.805%
No Solution: 446553 0.225%
Too Short: 0 0.000%
Fully Extended: 353199934 88.791%
Partly Extended: 23938583 6.018%
Not Extended: 20649433 5.191%
Adapters Expected: 584953 0.147%
Adapters Found: 135017 0.034%
Avg Insert: 146.5
Standard Deviation: 37.3
Mode: 125
Insert range: 35 - 241
90th percentile: 201
75th percentile: 171
50th percentile: 141
25th percentile: 118
10th percentile: 102
Export PNG
Creators and Submitter
Activity
Views: 456 Downloads: 41
Created: 16th May 2022 at 11:58
Last updated: 6th Nov 2024 at 15:26
AttributionsNone
Version History
Version 1 (earliest) Created 16th May 2022 at 11:58 by Marko Petek
No revision comments
Related items
Advanced People list for this Data file with search and filtering
https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
Advanced Programmes list for this Data file with search and filtering
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
Advanced Projects list for this Data file with search and filtering
SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.
Synthetic biology data management spreadsheet: https://fairdomhub.org/data_files/6036
Programme: NIBSys
Public web page: http://susphire.info/susphireproject/
Start date: 1st Apr 2018
End date: 30th Sep 2021
Advanced Investigations list for this Data file with search and filtering
Short Name: T31_mealybug Title: Mealybug genome and transcriptome analyses Description: Searching for enzymes involved in the mealybug pheromone biosynthesis pathways. These pheromones are known to be released by virgin females. Phenodata: ./phenodata_20190523.txt Featuredata: Principal investigator: Heribert Warzecha, Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_P3_expressionEcoli, _S_P4_AdPathGenes, _S_P4_Pcitri_IsoSeq, _S_P4_Pcitri_genome, _S_P4_Pcitri_genome_extSamples, _S_P4_Pcitri_tr1, _S_P4_Pcitri_tr1tr2combo, _S_P4_Pcitri_tr2, _S_P4_cand_all, _S_P4_cand_genomic
Assays: _A_01-CoEXpNetViz_tr2-coexpr, _A_01_NGI-IsoSeq, _A_01_RNAseq-CLC, _A_01_assembly2-rnaSPAdes, _A_01_mapToGenomeAll-STAR, _A_01_renameFASTA-Bioinfo, _A_02-CoEXpNetViz_gen-coexpr, _A_02_CDHIT-Bioinfo, _A_02_assembly2-IPS, _A_02_cDNAcupcake-dry, _A_02_limma-R, _A_02_mapToGenomeAll_limma-R, _A_03-IPS, _A_03_CDHIT2-Bioinfo, _A_03_limma_min50counts-R, _A_03_mapAs2ToGenome-STAR, _A_04_limma_min10counts-R, _A_04_mapIllumina-STAR, _A_04_mapReadsToAs2-STAR, _A_05_As2_tr_limmaDE-R, _A_05_DE_limma-R, _A_05_assembly1-rnaSPAdes, _A_06_assembly1-IPS, _A_07_mapAs1ToGenome-STAR, _A_08_mapReadsToAs1-STAR, _A_09_As1_tr_limmaDE-R, _A_C98F-EcoliExpr, _A_IDIsearch-Bioinfo, _A_IPS-bioinfo, _A_MAST-bioinfo, _A_MEME-bioinfo, _A_MSA-bioinfo, _A_MeUppS-EcoliExpr, _A_Node14610-EcoliExpr, _A_Node14610DmTP-EcoliExpr, _A_OtherMealybugCandidates-Alignment, _A_Pc1599-EcoliExpr, _A_Pc23180-EcoliExpr, _A_Pc2704-EcoliExpr, _A_Pc32607-EcoliExpr, _A_Pc7366II-EcoliExpr, _A_PcCis24-EcoliExpr, _A_Strep_CLDS-bioinfo, _A_TPS_phy-bioinfo, _A_Terzyme-bioinfo, _A_Trans1153-EcoliExpr, _A_Trans2-EcoliExpr, _A_Trans39-EcoliExpr, _A_Trans57-EcoliExpr, _A_Trans64-EcoliExpr, _A_Trans94-EcoliExpr, _A_candidatemining-bioinfo, _A_g14825_recon-bioinfo, _A_smallIDSsubunit-motifs, _I_T31_mealybug-files, _S_P3_expressionEcoli-files, _S_P4_AdPathGenes-files, _S_P4_Pcitri_IsoSeq-files, _S_P4_Pcitri_genome-files, _S_P4_Pcitri_genome_extSamples-files, _S_P4_Pcitri_tr1-files, _S_P4_Pcitri_tr1tr2combo-files, _S_P4_Pcitri_tr2-files, _S_P4_cand_all-files, _S_P4_cand_genomic-files
Advanced Studies list for this Data file with search and filtering
Short Name: P4_Pcitri_tr2 Description: Study of P. citri transcriptome data from SUSPHIRE and mealybug.org RNA-Seq datasets Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T31_mealybug
Assays: _A_01_assembly2-rnaSPAdes, _A_02_assembly2-IPS, _A_03_mapAs2ToGenome-STAR, _A_04_mapReadsToAs2-STAR, _A_05_As2_tr_limmaDE-R, _S_P4_Pcitri_tr2-files
Advanced Assays list for this Data file with search and filtering
Short Name: 01_assembly2-rnaSPAdes Assay Class: DRY Assay Type: rnaSPAdes Title: P citri de-novo transcriptome assembly 2 Description: P citri de-novo transcriptome assembly using SUSPHIRE and mealybug.org RNA-seq datasets pISA Assay creation date: 2019-05-24 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T31_mealybug
Study: _S_P4_Pcitri_tr2
