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comparison test-data/output_dedup_pairs_markdups.pairsam @ 2:6cbca5661205 draft

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planemo upload for repository https://github.com/open2c/pairtools commit 162c595b19e442f40be4c2f5434b20b56ade52d4
author iuc
date Tue, 30 Apr 2024 12:02:01 +0000
parents 3c87fa1a3b50
children
comparison
equal deleted inserted replaced
1:81fc1418fbfb 2:6cbca5661205
37 #samheader: @SQ SN:chrXV LN:1091291 37 #samheader: @SQ SN:chrXV LN:1091291
38 #samheader: @SQ SN:chrXVI LN:948066 38 #samheader: @SQ SN:chrXVI LN:948066
39 #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz 39 #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz
40 #samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa VN:1.0.2 40 #samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa VN:1.0.2
41 #samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-1.2 VN:1.0.2 41 #samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-1.2 VN:1.0.2
42 #samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-1.3 VN:1.0.2 42 #samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-1.3 VN:1.1.0
43 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz 43 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz
44 #samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-2CCE5976 VN:1.0.2 44 #samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-2CCE5976 VN:1.0.2
45 #samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-2.2 VN:1.0.2 45 #samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-2.2 VN:1.0.2
46 #samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-2.3 VN:1.0.2 46 #samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-2.3 VN:1.1.0
47 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz 47 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz
48 #samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-3CAFD9D9 VN:1.0.2 48 #samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-3CAFD9D9 VN:1.0.2
49 #samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-3.2 VN:1.0.2 49 #samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-3.2 VN:1.0.2
50 #samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-3.3 VN:1.0.2 50 #samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-3.3 VN:1.1.0
51 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz 51 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz
52 #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam 52 #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam
53 #samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:samtools VN:1.0.2 53 #samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:samtools VN:1.0.2
54 #samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-4.3 VN:1.0.2 54 #samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-4.3 VN:1.0.2
55 #samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-4.4 VN:1.0.2 55 #samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-4.4 VN:1.1.0
56 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 56 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2
57 HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU HWI-ST560:29:B0A7LABXX:2:1101:15566:2414197chrI31996015S35M=3350201CTTAGACAATAAGCTAGCTTTCAAGATATAAGATACGAAATAGGGGTTGA111442422223232232<FHIIIIBCCFHEHFHHIHCGIJIDHHJ?@FHNM:i:0MD:Z:35AS:i:35XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:15566:24141145chrI33506050M=3199-201TAGAATCTCCCATGTCAACGGGTTTCCATACCTCCCCAGCATCATACATCGHHGFAGFJJJIHHFGD?HIGCGHGHHHFAFC<IHFACHDAFDEDADB==NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU 57 HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU HWI-ST560:29:B0A7LABXX:2:1101:15566:2414197chrI31996015S35M=3350201CTTAGACAATAAGCTAGCTTTCAAGATATAAGATACGAAATAGGGGTTGA111442422223232232<FHIIIIBCCFHEHFHHIHCGIJIDHHJ?@FHNM:i:0MD:Z:35AS:i:35XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:15566:24141145chrI33506050M=3199-201TAGAATCTCCCATGTCAACGGGTTTCCATACCTCCCCAGCATCATACATCGHHGFAGFJJJIHHFGD?HIGCGHGHHHFAFC<IHFACHDAFDEDADB==NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU
58 HWI-ST560:29:B0A7LABXX:2:1101:18861:21891 chrI 35431 chrI 35703 + - UU HWI-ST560:29:B0A7LABXX:2:1101:18861:2189197chrI354316050M=35654273GACCACGTGGTCGTTGATGCTGCCAGCAGTTGTGCAGACCTGCATTGCTG114442222322<2@FEAFHFH<CFHFFH?GH:CDHGGIGEFDG<BBH9?NM:i:1MD:Z:35G14AS:i:45XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:18861:21891145chrI356546050M=35431-273ATGTGGCTGCTTTAATTGAGCCTCTTTCTGTCACCTGGCATGCTGTTAAG>EGDD?BFIIIIGBHCJIJIHFIHFHGHGGC<2GHGHFD<HFFDDDDB@BNM:i:1MD:Z:14G35AS:i:45XS:i:0Yt:Z:UU 58 HWI-ST560:29:B0A7LABXX:2:1101:18861:21891 chrI 35431 chrI 35703 + - UU HWI-ST560:29:B0A7LABXX:2:1101:18861:2189197chrI354316050M=35654273GACCACGTGGTCGTTGATGCTGCCAGCAGTTGTGCAGACCTGCATTGCTG114442222322<2@FEAFHFH<CFHFFH?GH:CDHGGIGEFDG<BBH9?NM:i:1MD:Z:35G14AS:i:45XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:18861:21891145chrI356546050M=35431-273ATGTGGCTGCTTTAATTGAGCCTCTTTCTGTCACCTGGCATGCTGTTAAG>EGDD?BFIIIIGBHCJIJIHFIHFHGHGGC<2GHGHFD<HFFDDDDB@BNM:i:1MD:Z:14G35AS:i:45XS:i:0Yt:Z:UU
59 HWUSI-EAS1533_0033_FC:1:1:2785:5545 chrI 50947 chrI 51201 + - UU HWUSI-EAS1533_0033_FC:1:1:2785:5545161chrI509476036M=51166255NAAATACCAAAGTCGAAAAATTTAGTACCCTGCAAA)444455777@CC@C@@CCCCCCCC@C@CCC@@@@@NM:i:1MD:Z:0T35AS:i:35XS:i:0Yt:Z:UU HWUSI-EAS1533_0033_FC:1:1:2785:554581chrI511666036M=50947-255TCAAGACATTAAGCATTACCTTAGGAGTCAAACTGG@CCCCCCC@CCC@@C@CCCC@CCCCC888888888DNM:i:0MD:Z:36AS:i:36XS:i:0Yt:Z:UU 59 HWUSI-EAS1533_0033_FC:1:1:2785:5545 chrI 50947 chrI 51201 + - UU HWUSI-EAS1533_0033_FC:1:1:2785:5545161chrI509476036M=51166255NAAATACCAAAGTCGAAAAATTTAGTACCCTGCAAA)444455777@CC@C@@CCCCCCCC@C@CCC@@@@@NM:i:1MD:Z:0T35AS:i:35XS:i:0Yt:Z:UU HWUSI-EAS1533_0033_FC:1:1:2785:554581chrI511666036M=50947-255TCAAGACATTAAGCATTACCTTAGGAGTCAAACTGG@CCCCCCC@CCC@@C@CCCC@CCCCC888888888DNM:i:0MD:Z:36AS:i:36XS:i:0Yt:Z:UU
60 HWI-ST560:29:B0A7LABXX:2:1101:19121:14576 chrI 85708 chrI 85934 + - UU HWI-ST560:29:B0A7LABXX:2:1101:19121:1457697chrI857086050M=85885227TAACCTCTAAATACAGAGCCTTATCTCTTTCTAGCTTTTCTTTTAAATTC11:=422222222234AFGFCHHHIIAAHGFFHGGHIJGGFHFCFGB?BFNM:i:1MD:Z:43C6AS:i:45XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:19121:14576145chrI858856050M=85708-227TAAACAATTCCACAACTAAACCAGGTTGAAGGTGGAAAATGGGAGTTCTTIIIGFBBHGIHGHCG?GHGHIGCAHFAIIIHIACGFCFHHHHFFDDABB@NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU 60 HWI-ST560:29:B0A7LABXX:2:1101:19121:14576 chrI 85708 chrI 85934 + - UU HWI-ST560:29:B0A7LABXX:2:1101:19121:1457697chrI857086050M=85885227TAACCTCTAAATACAGAGCCTTATCTCTTTCTAGCTTTTCTTTTAAATTC11:=422222222234AFGFCHHHIIAAHGFFHGGHIJGGFHFCFGB?BFNM:i:1MD:Z:43C6AS:i:45XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:19121:14576145chrI858856050M=85708-227TAAACAATTCCACAACTAAACCAGGTTGAAGGTGGAAAATGGGAGTTCTTIIIGFBBHGIHGHCG?GHGHIGCAHFAIIIHIACGFCFHHHHFFDDABB@NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU