Mercurial > repos > jjohnson > bamutil_diff
comparison test-data/diff_only1_in1.sam @ 0:2cafa8420c04 draft default tip
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/bamutil/ commit c1945909ca200610f128577b68a82d9228905f3d-dirty"
| author | jjohnson |
|---|---|
| date | Fri, 26 Mar 2021 13:16:53 +0000 |
| parents | |
| children |
comparison
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| -1:000000000000 | 0:2cafa8420c04 |
|---|---|
| 1 @HD VN:1.0 SO:coordinate | |
| 2 @SQ SN:1 LN:248956422 | |
| 3 @SQ SN:2 LN:242193529 | |
| 4 @SQ SN:3 LN:198295559 | |
| 5 @SQ SN:4 LN:190214555 | |
| 6 @SQ SN:5 LN:181538259 | |
| 7 @SQ SN:6 LN:170805979 | |
| 8 @SQ SN:7 LN:159345973 | |
| 9 @SQ SN:8 LN:145138636 | |
| 10 @SQ SN:9 LN:138394717 | |
| 11 @SQ SN:10 LN:133797422 | |
| 12 @SQ SN:11 LN:135086622 | |
| 13 @SQ SN:12 LN:133275309 | |
| 14 @SQ SN:13 LN:114364328 | |
| 15 @SQ SN:14 LN:107043718 | |
| 16 @SQ SN:15 LN:101991189 | |
| 17 @SQ SN:16 LN:90338345 | |
| 18 @SQ SN:17 LN:83257441 | |
| 19 @SQ SN:18 LN:80373285 | |
| 20 @SQ SN:19 LN:58617616 | |
| 21 @SQ SN:20 LN:64444167 | |
| 22 @SQ SN:21 LN:46709983 | |
| 23 @SQ SN:22 LN:50818468 | |
| 24 @SQ SN:X LN:156040895 | |
| 25 @SQ SN:Y LN:57227415 | |
| 26 @SQ SN:MT LN:16569 | |
| 27 @PG ID:hisat2 PN:hisat2 VN:2.1.0 CL:"/panfs/roc/galaxy/shared/miniconda3/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/risdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq" | |
| 28 @PG ID:hisat2-55424A4 PN:hisat2 VN:2.1.0 CL:"/home/galaxy/galaxy/miniconda2/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq" | |
| 29 @PG ID:hisat2-55424A4-3A2CCEF5 PN:hisat2 VN:2.1.0 CL:"/panfs/roc/galaxy/shared/miniconda3/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/risdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq" | |
| 30 @PG ID:samtools PN:samtools PP:hisat2-55424A4-3A2CCEF5 VN:1.11 CL:samtools sort -@ 1 -m 10240M -T sorttemp -O sam -o 0.sam /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075444.dat | |
| 31 @PG ID:hisat2-3A2CCEF5 PN:hisat2 VN:2.1.0 CL:"/home/galaxy/galaxy/miniconda2/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/rissdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq" | |
| 32 @PG ID:samtools-6ADB4A65 PN:samtools PP:hisat2-3A2CCEF5 VN:1.11 CL:samtools sort -@ 1 -m 10240M -T sorttemp -O sam -o 1.sam /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075446.dat | |
| 33 @PG ID:samtools.1 PN:samtools PP:samtools VN:1.11 CL:samtools merge -@ 1 -s 1 -f -h /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075446.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075450.dat 0.sam 1.sam | |
| 34 @PG ID:samtools.2 PN:samtools PP:samtools-6ADB4A65 VN:1.11 CL:samtools merge -@ 1 -s 1 -f -h /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075446.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075450.dat 0.sam 1.sam | |
| 35 @PG ID:hisat2-6ADB4A65 PN:hisat2 VN:2.1.0 CL:"/panfs/roc/galaxy/shared/miniconda3/envs/mulled-v1-e7321ba46fa5ea4c6b9a06b78e6cd5182b33c0a47c2c86b5d610e1361f8b1686/bin/hisat2-align-s --wrapper basic-0 -p 4 -x /panfs/roc/risdb/galaxy/genomes/GRCh38_canon/hisat2_index/GRCh38_canon/GRCh38_canon --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --known-splicesite-infile splice_sites.txt --min-intronlen 20 --max-intronlen 500000 --dta -1 input_f.fastq -2 input_r.fastq" | |
| 36 @PG ID:samtools.3 PN:samtools PP:samtools.1 VN:1.11 CL:samtools merge -@ 1 -s 1 -f -h /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075454.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075523.dat 0.sam 1.sam | |
| 37 @PG ID:samtools.4 PN:samtools PP:samtools.2 VN:1.11 CL:samtools merge -@ 1 -s 1 -f -h /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075454.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/075/dataset_1075523.dat 0.sam 1.sam | |
| 38 NB500964:249:HHLFNBGX7:1:12312:5087:3846 163 6 52995649 60 75M = 52995848 274 TGTCACCCCATTGATCGCCAGGGTTGATTCGGCTGATCTGGCTGGCTAGGCGGGTGTCCCCTTCCTCCCTCACCG AAAA/EEEE6EEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEE6EEEEEEEE/EEEEEEEEEEEEEEEEEE/EE/ AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 ZS:i:-1 XO:i:0 XG:i:0 YS:i:-2 YT:Z:CP | |
| 39 NB500964:249:HHLFNBGX7:2:23304:14989:7965 129 6 52995665 1 75M 2 32916255 0 GCCAGGGTTGATTCGGCTGATCTGGCTGGCTAGGCGGGTGTCCCCTTCCTCCCTCACCGCTCCATGTGCGTCCCT AAAAAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEE<AE AS:i:0 MD:Z:75 NM:i:0 NH:i:2 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YT:Z:UP | |
| 40 NB500964:249:HHLFNBGX7:4:13611:22454:15447 419 6 52995667 1 75M = 52995712 120 CAGGGTTGATTCGGCTGATCTGGCTGGCTAGGCGGGTGTCCCCTTCCTCCCTCACCGCTCCATGTGCGTCCCTCC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEE AS:i:0 MD:Z:75 NM:i:0 NH:i:2 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 41 NB500964:249:HHLFNBGX7:3:12409:4568:1161 163 6 52995706 60 75M = 52995785 154 CCCCTTCCTCCCTCACCGCTCCATGTGCGTCCCTCCCGAAGCTGCGCGCTCGGTCGAAGAGGACGACCATCCCCG AA/AAEEAEEAAAAEEAEEEEEEEEEEE/EEAEEEEEEEAEEEE<EEAEEEEEEEAA<EEAE<AA/AEAEAEEAA AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 42 NB500964:249:HHLFNBGX7:4:21406:23062:17974 163 6 52995706 60 75M = 52995825 194 CCCCTTCCTCCCTCACCGCTCCATGTGCGTCCCTCCCGAAGCTGCGCGCTCGGTCGAAGAGGACGACCATCCCCG AAAAAEEEEEAEEEEAEEEAEEAAEEEEE/AEEEEE<EAEAEEEEEEEEEA/EEEEEEAEEEEAE<EE6E<E6EE AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 43 NB500964:249:HHLFNBGX7:4:13611:22454:15447 339 6 52995712 1 75M = 52995667 -120 CCTCCCTCACCGCTCCATGTGCGTCCCTCCCGAAGCTGCGCGCTCGGTCGAAGAGGACGACCATCCCCGATAGAG EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA AS:i:0 MD:Z:75 NM:i:0 NH:i:2 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 44 NB500964:249:HHLFNBGX7:3:23507:21978:1662 163 6 52995758 60 75M = 52995835 151 GTCGAAGAGGACGACCATCCCCGATAGAGGAGGACCTGTCTTCGGTCAAGGGTATACTAGTAGCTGCGCTCCCCT AA/AAEEE6EAEEEAEEEEEEAEEE6EEE/EEA/EA/E/EEEEEEEEEEAEEEEEEE/E/66/<E<A<A6A//// AS:i:-6 MD:Z:36G20G17 NM:i:2 NH:i:1 XN:i:0 XM:i:2 ZS:i:-6 XO:i:0 XG:i:0 YS:i:-8 YT:Z:CP | |
| 45 NB500964:249:HHLFNBGX7:2:11209:14749:12659 163 6 52995766 60 75M = 52995834 143 GGACGACCATCCCCGATAGAGGAGGACCGGTCTTCGGTCAAGGGTATACGAGTAGCTGCGCTCCCCTGCTAGAAC AAAAA/EEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEAE<EEAEEEEEEE<6E AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 46 NB500964:249:HHLFNBGX7:3:12409:4568:1161 83 6 52995785 60 75M = 52995706 -154 AGGAGGACCGGTCTTCGGTCAAGGGTATACGAGTAGCTGCGCTCCCCTGCTAGAACCTCCAAACAAGCTCTCAAG </EA<AEEE/EAAEEAAEAE/EEEEEEEEEAEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAAA AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 47 NB500964:249:HHLFNBGX7:4:21406:23062:17974 83 6 52995825 60 75M = 52995706 -194 GCTCCCCTGCTAGAACCTCCAAACAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAG EAEEA<<A/EEEEE/EEEEEEEEEEEEEE/EEAE/EEEEEE/EAEE<AEAEEEEEEEEEEEAAA/EEEEEA6AAA AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 48 NB500964:249:HHLFNBGX7:2:13103:3678:13730 89 6 52995829 60 75M = 52995829 0 CCCTGCTAGAACCTCCAAACAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAGACTC EEEEEEEAAEEEEAAEEEEAEAEEEEEEEEEE/EEEEEEEEEEAEEEAEEEEAEEEEEEEE6EAEEEAAEAAAAA AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 XO:i:0 XG:i:0 YT:Z:UP | |
| 49 NB500964:249:HHLFNBGX7:2:11209:14749:12659 83 6 52995834 60 75M = 52995766 -143 CTAGAACCTCCAAACAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGAC EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 50 NB500964:249:HHLFNBGX7:3:23507:21978:1662 83 6 52995835 60 1S73M1S = 52995758 -151 GTAGAACCTCCAAACAATCTCTCAAGGTCCATTTGTAGGAGAACGTAGTGTAGTCAAGCTTCCAAGACTCCAGAA //E/EE/A/6/E/E/EE//E/E/E/<6EE/EAEE//E<A/EE///EEA/EEEEEEEAE6EEEEAEAE6EEAAA6A AS:i:-8 MD:Z:16G30G25 NM:i:2 NH:i:1 XN:i:0 XM:i:2 XO:i:0 XG:i:0 YS:i:-6 YT:Z:CP | |
| 51 NB500964:249:HHLFNBGX7:4:12611:5420:13168 81 6 52995838 60 74M1S 2 32916257 0 AACCTCCAAACAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGACACAC EEEEAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEAAAAA AS:i:-1 MD:Z:74 NM:i:0 NH:i:1 XN:i:0 XM:i:0 XO:i:0 XG:i:0 YT:Z:UP | |
| 52 NB500964:249:HHLFNBGX7:1:12312:5087:3846 83 6 52995848 60 73M2S = 52995649 -274 CAAGCTCTCAAGGTCCATTTGTAGGAGAACGTAGGGTAGTCAAGCTTCCAAGACTCCAGACACATCCAAATGAAG <EEEEEEEEEEEEAEEEEEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA AS:i:-2 MD:Z:73 NM:i:0 NH:i:1 XN:i:0 XM:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 53 NB500964:249:HHLFNBGX7:3:21607:1536:15142 99 6 73518202 60 63M89N12M = 73518250 118 GTGGCAATCCAATACAGGGGCATAGCCGGCGCTTATTTGGCCTGGATGGTTCAGGATAATCACCTGAGCAGTGAA AAAAAEEEEEEEEEEEAEEA/EEEEAEAEAEEEEEEEAEEE<EAA/EEEEE<EEAE/EA</A/AAAAAEAA/E/< AS:i:0 MD:Z:75 NM:i:0 NH:i:1 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:-2 YT:Z:CP XS:A:- | |
| 54 NB500964:249:HHLFNBGX7:3:21607:1536:15142 147 6 73518250 60 2S15M89N58M = 73518202 -118 TTGTTCAGGATAATCACCTGAGCAGTGAAGCCAGCTGCTTCCATTGGTGGGTCATTTTTGCTGTCACCAGCAACG A/<EAEEA//<//EA/AEAEE/EEA//EE<EEE/EEA/AEEEEEAAAEE/E/EEEEEEEEEEE/EEEEEEAAAAA AS:i:-2 MD:Z:73 NM:i:0 NH:i:1 XN:i:0 XM:i:0 ZS:i:-2 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP XS:A:- | |
| 55 NB500964:249:HHLFNBGX7:2:21106:19199:5423 99 6 73519036 1 75M = 73519096 135 CCTTAACAATTTCCTCATATCTCTTCTGGCTGTAGGGTGGCTCAGTGGAATCCATTTTGTTAACACCGACAATTA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE AS:i:0 MD:Z:75 NM:i:0 NH:i:3 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 56 NB500964:249:HHLFNBGX7:2:21106:19199:5423 147 6 73519096 1 75M = 73519036 -135 TAACACCGACAATTAGTTGTTTCACACCCAGTGTGTAAGCCAGAAGGGCATGCTCTCGGGTCTGCCCATTCTTGG EEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEAAAAA AS:i:0 MD:Z:75 NM:i:0 NH:i:3 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 57 NB500964:249:HHLFNBGX7:1:23112:23126:11688 355 6 73519370 1 75M = 73519434 139 GTCTCTGTGTCCTGGGGCATCAATGATAGTCACATAGTACTTGCTGGTCTCAAATTTCCACAAGGAGATATCAAT AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEEEEEEEEEE AS:i:0 MD:Z:75 NM:i:0 NH:i:2 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP | |
| 58 NB500964:249:HHLFNBGX7:1:23112:23126:11688 403 6 73519434 1 75M = 73519370 -139 GAGATATCAATGGTGATACCACGTTCACGCTCAGCTTTCAGTTTATCCAAGACCCAGGCATACTTGAAGGAGCCC EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEAEEEEEEEEEEEEAAAAA AS:i:0 MD:Z:75 NM:i:0 NH:i:2 XN:i:0 XM:i:0 ZS:i:0 XO:i:0 XG:i:0 YS:i:0 YT:Z:CP |