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August 18, 2020 22:27
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| @HD VN:1.6 SO:coordinate | |
| @SQ SN:chr1 LN:248956422 | |
| @SQ SN:chr10 LN:133797422 | |
| @SQ SN:chr11 LN:135086622 | |
| @SQ SN:chr12 LN:133275309 | |
| @SQ SN:chr13 LN:114364328 | |
| @SQ SN:chr14 LN:107043718 | |
| @SQ SN:chr15 LN:101991189 | |
| @SQ SN:chr16 LN:90338345 | |
| @SQ SN:chr17 LN:83257441 | |
| @SQ SN:chr18 LN:80373285 | |
| @SQ SN:chr19 LN:58617616 | |
| @SQ SN:chr2 LN:242193529 | |
| @SQ SN:chr20 LN:64444167 | |
| @SQ SN:chr21 LN:46709983 | |
| @SQ SN:chr22 LN:50818468 | |
| @SQ SN:chr3 LN:198295559 | |
| @SQ SN:chr4 LN:190214555 | |
| @SQ SN:chr5 LN:181538259 | |
| @SQ SN:chr6 LN:170805979 | |
| @SQ SN:chr7 LN:159345973 | |
| @SQ SN:chr8 LN:145138636 | |
| @SQ SN:chr9 LN:138394717 | |
| @SQ SN:chrM LN:16569 | |
| @SQ SN:chrX LN:156040895 | |
| @SQ SN:chrY LN:57227415 | |
| @SQ SN:KI270728.1 LN:1872759 | |
| @SQ SN:KI270727.1 LN:448248 | |
| @SQ SN:KI270442.1 LN:392061 | |
| @SQ SN:KI270729.1 LN:280839 | |
| @SQ SN:GL000225.1 LN:211173 | |
| @SQ SN:KI270743.1 LN:210658 | |
| @SQ SN:GL000008.2 LN:209709 | |
| @SQ SN:GL000009.2 LN:201709 | |
| @SQ SN:KI270747.1 LN:198735 | |
| @SQ SN:KI270722.1 LN:194050 | |
| @SQ SN:GL000194.1 LN:191469 | |
| @SQ SN:KI270742.1 LN:186739 | |
| @SQ SN:GL000205.2 LN:185591 | |
| @SQ SN:GL000195.1 LN:182896 | |
| @SQ SN:KI270736.1 LN:181920 | |
| @SQ SN:KI270733.1 LN:179772 | |
| @SQ SN:GL000224.1 LN:179693 | |
| @SQ SN:GL000219.1 LN:179198 | |
| @SQ SN:KI270719.1 LN:176845 | |
| @SQ SN:GL000216.2 LN:176608 | |
| @SQ SN:KI270712.1 LN:176043 | |
| @SQ SN:KI270706.1 LN:175055 | |
| @SQ SN:KI270725.1 LN:172810 | |
| @SQ SN:KI270744.1 LN:168472 | |
| @SQ SN:KI270734.1 LN:165050 | |
| @SQ SN:GL000213.1 LN:164239 | |
| @SQ SN:GL000220.1 LN:161802 | |
| @SQ SN:KI270715.1 LN:161471 | |
| @SQ SN:GL000218.1 LN:161147 | |
| @SQ SN:KI270749.1 LN:158759 | |
| @SQ SN:KI270741.1 LN:157432 | |
| @SQ SN:GL000221.1 LN:155397 | |
| @SQ SN:KI270716.1 LN:153799 | |
| @SQ SN:KI270731.1 LN:150754 | |
| @SQ SN:KI270751.1 LN:150742 | |
| @SQ SN:KI270750.1 LN:148850 | |
| @SQ SN:KI270519.1 LN:138126 | |
| @SQ SN:GL000214.1 LN:137718 | |
| @SQ SN:KI270708.1 LN:127682 | |
| @SQ SN:KI270730.1 LN:112551 | |
| @SQ SN:KI270438.1 LN:112505 | |
| @SQ SN:KI270737.1 LN:103838 | |
| @SQ SN:KI270721.1 LN:100316 | |
| @SQ SN:KI270738.1 LN:99375 | |
| @SQ SN:KI270748.1 LN:93321 | |
| @SQ SN:KI270435.1 LN:92983 | |
| @SQ SN:GL000208.1 LN:92689 | |
| @SQ SN:KI270538.1 LN:91309 | |
| @SQ SN:KI270756.1 LN:79590 | |
| @SQ SN:KI270739.1 LN:73985 | |
| @SQ SN:KI270757.1 LN:71251 | |
| @SQ SN:KI270709.1 LN:66860 | |
| @SQ SN:KI270746.1 LN:66486 | |
| @SQ SN:KI270753.1 LN:62944 | |
| @SQ SN:KI270589.1 LN:44474 | |
| @SQ SN:KI270726.1 LN:43739 | |
| @SQ SN:KI270735.1 LN:42811 | |
| @SQ SN:KI270711.1 LN:42210 | |
| @SQ SN:KI270745.1 LN:41891 | |
| @SQ SN:KI270714.1 LN:41717 | |
| @SQ SN:KI270732.1 LN:41543 | |
| @SQ SN:KI270713.1 LN:40745 | |
| @SQ SN:KI270754.1 LN:40191 | |
| @SQ SN:KI270710.1 LN:40176 | |
| @SQ SN:KI270717.1 LN:40062 | |
| @SQ SN:KI270724.1 LN:39555 | |
| @SQ SN:KI270720.1 LN:39050 | |
| @SQ SN:KI270723.1 LN:38115 | |
| @SQ SN:KI270718.1 LN:38054 | |
| @SQ SN:KI270317.1 LN:37690 | |
| @SQ SN:KI270740.1 LN:37240 | |
| @SQ SN:KI270755.1 LN:36723 | |
| @SQ SN:KI270707.1 LN:32032 | |
| @SQ SN:KI270579.1 LN:31033 | |
| @SQ SN:KI270752.1 LN:27745 | |
| @SQ SN:KI270512.1 LN:22689 | |
| @SQ SN:KI270322.1 LN:21476 | |
| @SQ SN:GL000226.1 LN:15008 | |
| @SQ SN:KI270311.1 LN:12399 | |
| @SQ SN:KI270366.1 LN:8320 | |
| @SQ SN:KI270511.1 LN:8127 | |
| @SQ SN:KI270448.1 LN:7992 | |
| @SQ SN:KI270521.1 LN:7642 | |
| @SQ SN:KI270581.1 LN:7046 | |
| @SQ SN:KI270582.1 LN:6504 | |
| @SQ SN:KI270515.1 LN:6361 | |
| @SQ SN:KI270588.1 LN:6158 | |
| @SQ SN:KI270591.1 LN:5796 | |
| @SQ SN:KI270522.1 LN:5674 | |
| @SQ SN:KI270507.1 LN:5353 | |
| @SQ SN:KI270590.1 LN:4685 | |
| @SQ SN:KI270584.1 LN:4513 | |
| @SQ SN:KI270320.1 LN:4416 | |
| @SQ SN:KI270382.1 LN:4215 | |
| @SQ SN:KI270468.1 LN:4055 | |
| @SQ SN:KI270467.1 LN:3920 | |
| @SQ SN:KI270362.1 LN:3530 | |
| @SQ SN:KI270517.1 LN:3253 | |
| @SQ SN:KI270593.1 LN:3041 | |
| @SQ SN:KI270528.1 LN:2983 | |
| @SQ SN:KI270587.1 LN:2969 | |
| @SQ SN:KI270364.1 LN:2855 | |
| @SQ SN:KI270371.1 LN:2805 | |
| @SQ SN:KI270333.1 LN:2699 | |
| @SQ SN:KI270374.1 LN:2656 | |
| @SQ SN:KI270411.1 LN:2646 | |
| @SQ SN:KI270414.1 LN:2489 | |
| @SQ SN:KI270510.1 LN:2415 | |
| @SQ SN:KI270390.1 LN:2387 | |
| @SQ SN:KI270375.1 LN:2378 | |
| @SQ SN:KI270420.1 LN:2321 | |
| @SQ SN:KI270509.1 LN:2318 | |
| @SQ SN:KI270315.1 LN:2276 | |
| @SQ SN:KI270302.1 LN:2274 | |
| @SQ SN:KI270518.1 LN:2186 | |
| @SQ SN:KI270530.1 LN:2168 | |
| @SQ SN:KI270304.1 LN:2165 | |
| @SQ SN:KI270418.1 LN:2145 | |
| @SQ SN:KI270424.1 LN:2140 | |
| @SQ SN:KI270417.1 LN:2043 | |
| @SQ SN:KI270508.1 LN:1951 | |
| @SQ SN:KI270303.1 LN:1942 | |
| @SQ SN:KI270381.1 LN:1930 | |
| @SQ SN:KI270529.1 LN:1899 | |
| @SQ SN:KI270425.1 LN:1884 | |
| @SQ SN:KI270396.1 LN:1880 | |
| @SQ SN:KI270363.1 LN:1803 | |
| @SQ SN:KI270386.1 LN:1788 | |
| @SQ SN:KI270465.1 LN:1774 | |
| @SQ SN:KI270383.1 LN:1750 | |
| @SQ SN:KI270384.1 LN:1658 | |
| @SQ SN:KI270330.1 LN:1652 | |
| @SQ SN:KI270372.1 LN:1650 | |
| @SQ SN:KI270548.1 LN:1599 | |
| @SQ SN:KI270580.1 LN:1553 | |
| @SQ SN:KI270387.1 LN:1537 | |
| @SQ SN:KI270391.1 LN:1484 | |
| @SQ SN:KI270305.1 LN:1472 | |
| @SQ SN:KI270373.1 LN:1451 | |
| @SQ SN:KI270422.1 LN:1445 | |
| @SQ SN:KI270316.1 LN:1444 | |
| @SQ SN:KI270340.1 LN:1428 | |
| @SQ SN:KI270338.1 LN:1428 | |
| @SQ SN:KI270583.1 LN:1400 | |
| @SQ SN:KI270334.1 LN:1368 | |
| @SQ SN:KI270429.1 LN:1361 | |
| @SQ SN:KI270393.1 LN:1308 | |
| @SQ SN:KI270516.1 LN:1300 | |
| @SQ SN:KI270389.1 LN:1298 | |
| @SQ SN:KI270466.1 LN:1233 | |
| @SQ SN:KI270388.1 LN:1216 | |
| @SQ SN:KI270544.1 LN:1202 | |
| @SQ SN:KI270310.1 LN:1201 | |
| @SQ SN:KI270412.1 LN:1179 | |
| @SQ SN:KI270395.1 LN:1143 | |
| @SQ SN:KI270376.1 LN:1136 | |
| @SQ SN:KI270337.1 LN:1121 | |
| @SQ SN:KI270335.1 LN:1048 | |
| @SQ SN:KI270378.1 LN:1048 | |
| @SQ SN:KI270379.1 LN:1045 | |
| @SQ SN:KI270329.1 LN:1040 | |
| @SQ SN:KI270419.1 LN:1029 | |
| @SQ SN:KI270336.1 LN:1026 | |
| @SQ SN:KI270312.1 LN:998 | |
| @SQ SN:KI270539.1 LN:993 | |
| @SQ SN:KI270385.1 LN:990 | |
| @SQ SN:KI270423.1 LN:981 | |
| @SQ SN:KI270392.1 LN:971 | |
| @SQ SN:KI270394.1 LN:970 | |
| @RG ID:1042128_1044472__OR-100-381:1042128_1044472:1:HJ2W5DSXY:1 SM:1042128_1044472__OR-100-381 LB:1042128_1044472.1 PU:1042128_1044472__OR-100-381:1042128_1044472:1:HJ2W5DSXY:1 PL:ILLUMINA | |
| @RG ID:1042128_1044472__OR-100-381:1042128_1044472:1:HJ2W5DSXY:2 SM:1042128_1044472__OR-100-381 LB:1042128_1044472.1 PU:1042128_1044472__OR-100-381:1042128_1044472:1:HJ2W5DSXY:2 PL:ILLUMINA | |
| @RG ID:1042128_1044472__OR-100-381:1042128_1044472:1:HJ2W5DSXY:3 SM:1042128_1044472__OR-100-381 LB:1042128_1044472.1 PU:1042128_1044472__OR-100-381:1042128_1044472:1:HJ2W5DSXY:3 PL:ILLUMINA | |
| @RG ID:1042128_1044472__OR-100-381:1042128_1044472:1:HJ2W5DSXY:4 SM:1042128_1044472__OR-100-381 LB:1042128_1044472.1 PU:1042128_1044472__OR-100-381:1042128_1044472:1:HJ2W5DSXY:4 PL:ILLUMINA | |
| @PG PN:bwa ID:bwa VN:0.7.17-r1188 CL:bwa mem -p -t 4 -M -R @RG\tID:1042128_1044472__OR-100-381:1042128_1044472:1:HJ2W5DSXY:1\tSM:1042128_1044472__OR-100-381\tLB:1042128_1044472.1\tPU:1042128_1044472__OR-100-381:1042128_1044472:1:HJ2W5DSXY:1\tPL:ILLUMINA /mnt/test/refdata/cs_references/GRCh38/fasta/genome.fa /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_ALIGNER/TRIM_READS/fork0/chnk0-u8c472ba8f2/files/read1.fastq | |
| @PG PN:samtools ID:samtools VN:1.10 PP:bwa CL:samtools view -bSh - | |
| @PG PN:cellranger-atac.attach_bcs ID:attach_bcs VN:2020.0804.1-17-g43e193b7c PP:samtools | |
| @PG PN:samtools ID:samtools.1 VN:1.10 (pysam) PP:attach_bcs CL:samtools sort -o /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk000-u8c472bd558/files/tagsorted_bam.bam -t GP /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/ATTACH_BCS/fork0/chnk000-u8c472bcbff/files/chunk_bam.bam | |
| @PG PN:samtools ID:samtools.2 VN:1.10 (pysam) PP:samtools.1 CL:samtools merge -t GP -c -p -s 0 -@ 4 /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/join-u8c472bd529/files/tagsorted_bam.bam /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk000-u8c472bd558/files/tagsorted_bam.bam /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk001-u8c472bd558/files/tagsorted_bam.bam /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk002-u8c472bd558/files/tagsorted_bam.bam /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk003-u8c472bd558/files/tagsorted_bam.bam /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk004-u8c472bd558/files/tagsorted_bam.bam /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk005-u8c472bd558/files/tagsorted_bam.bam /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk006-u8c472bd558/files/tagsorted_bam.bam /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk007-u8c472bd558/files/tagsorted_bam.bam /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk008-u8c472bd558/files/tagsorted_bam.bam /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk009-u8c472bd558/files/tagsorted_bam.bam /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk010-u8c472bd56c/files/tagsorted_bam.bam /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk011-u8c472bd56c/files/tagsorted_bam.bam /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk012-u8c472bd56c/files/tagsorted_bam.bam /mnt/freezer-qa/freezer/cellranger-arc-pd/43e193b7c738a7c657396d1922c3c27e86e258a5/atac_gex_OR-100-381/OR-100-381/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_ATAC_MATRIX_COMPUTER/_SORT_AND_MARK_DUPS/SORT_READS_BY_POS/fork0/chnk013-u8c472bd56c/files/tagsorted_bam.bam 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| @CO 10x_bam_to_fastq:R1(SEQ:QUAL,TR:TQ) | |
| @CO 10x_bam_to_fastq:R2(SEQ:QUAL,TR:TQ) | |
| @CO 10x_bam_to_fastq:I1(BC:QT) | |
| @CO 10x_bam_to_fastq:I2(CR:CY) | |
| @CO 10x_bam_to_fastq_seqnames:R1,R3,I1,R2 |
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