sending incremental file list zr3534_10_R1.fq.gz zr3534_10_R2.fq.gz zr3534_1_R1.fq.gz zr3534_1_R2.fq.gz zr3534_2_R1.fq.gz zr3534_2_R2.fq.gz zr3534_3_R1.fq.gz zr3534_3_R2.fq.gz zr3534_4_R1.fq.gz zr3534_4_R2.fq.gz zr3534_5_R1.fq.gz zr3534_5_R2.fq.gz zr3534_6_R1.fq.gz zr3534_6_R2.fq.gz zr3534_7_R1.fq.gz zr3534_7_R2.fq.gz zr3534_8_R1.fq.gz zr3534_8_R2.fq.gz zr3534_9_R1.fq.gz zr3534_9_R2.fq.gz sent 89,686,651,025 bytes received 396 bytes 349,655,561.10 bytes/sec total size is 89,664,758,956 speedup is 1.00 Detecting adapter sequence for read1... No adapter detected for read1 Detecting adapter sequence for read2... No adapter detected for read2 WARNING: fastp uses up to 16 threads although you specified 27 Read1 before filtering: total reads: 79094628 total bases: 9980662363 Q20 bases: 9686649572(97.0542%) Q30 bases: 9102203279(91.1984%) Read2 before filtering: total reads: 79094628 total bases: 9976863161 Q20 bases: 9624030897(96.4635%) Q30 bases: 8988679673(90.0952%) Read1 after filtering: total reads: 77718463 total bases: 8676155201 Q20 bases: 8428717248(97.1481%) Q30 bases: 7912221784(91.195%) Read2 aftering filtering: total reads: 77718463 total bases: 8670532075 Q20 bases: 8371385807(96.5499%) Q30 bases: 7801671756(89.9792%) Filtering result: reads passed filter: 155436926 reads failed due to low quality: 1035406 reads failed due to too many N: 27894 reads failed due to too short: 1689030 reads with adapter trimmed: 60081484 bases trimmed due to adapters: 694687948 Duplication rate: 17.0699% Insert size peak (evaluated by paired-end reads): 20 JSON report: zr3534_10_R1.fastp-trim.20201130.report.json HTML report: zr3534_10_R1.fastp-trim.20201130.report.html /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 zr3534_10_R1.fq.gz --in2 zr3534_10_R2.fq.gz --detect_adapter_for_pe --detect_adapter_for_pe --trim_front1 10 --trim_front2 10 --thread 27 --html zr3534_10_R1.fastp-trim.20201130.report.html --json zr3534_10_R1.fastp-trim.20201130.report.json --out1 zr3534_10_R1.fastp-trim.20201130.fq.gz --out2 zr3534_10_R2.fastp-trim.20201130.fq.gz fastp v0.20.0, time used: 812 seconds Detecting adapter sequence for read1... No adapter detected for read1 Detecting adapter sequence for read2... No adapter detected for read2 WARNING: fastp uses up to 16 threads although you specified 27 Read1 before filtering: total reads: 78029780 total bases: 9842948370 Q20 bases: 9541128329(96.9336%) Q30 bases: 8948130052(90.909%) Read2 before filtering: total reads: 78029780 total bases: 9837794545 Q20 bases: 9482418951(96.3876%) Q30 bases: 8842606439(89.884%) Read1 after filtering: total reads: 76660065 total bases: 8559127686 Q20 bases: 8306529429(97.0488%) Q30 bases: 7782385725(90.925%) Read2 aftering filtering: total reads: 76660065 total bases: 8552530157 Q20 bases: 8250136381(96.4643%) Q30 bases: 7675186321(89.7417%) Filtering result: reads passed filter: 153320130 reads failed due to low quality: 1054344 reads failed due to too many N: 27222 reads failed due to too short: 1657864 reads with adapter trimmed: 58004260 bases trimmed due to adapters: 675322010 Duplication rate: 17.3857% Insert size peak (evaluated by paired-end reads): 20 JSON report: zr3534_1_R1.fastp-trim.20201130.report.json HTML report: zr3534_1_R1.fastp-trim.20201130.report.html /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 zr3534_1_R1.fq.gz --in2 zr3534_1_R2.fq.gz --detect_adapter_for_pe --detect_adapter_for_pe --trim_front1 10 --trim_front2 10 --thread 27 --html zr3534_1_R1.fastp-trim.20201130.report.html --json zr3534_1_R1.fastp-trim.20201130.report.json --out1 zr3534_1_R1.fastp-trim.20201130.fq.gz --out2 zr3534_1_R2.fastp-trim.20201130.fq.gz fastp v0.20.0, time used: 873 seconds Detecting adapter sequence for read1... No adapter detected for read1 Detecting adapter sequence for read2... No adapter detected for read2 WARNING: fastp uses up to 16 threads although you specified 27 Read1 before filtering: total reads: 76804380 total bases: 9705417777 Q20 bases: 9421235822(97.0719%) Q30 bases: 8859564646(91.2847%) Read2 before filtering: total reads: 76804380 total bases: 9701899383 Q20 bases: 9338099468(96.2502%) Q30 bases: 8692535285(89.5962%) Read1 after filtering: total reads: 75548753 total bases: 8458453351 Q20 bases: 8221435730(97.1979%) Q30 bases: 7724277028(91.3202%) Read2 aftering filtering: total reads: 75548753 total bases: 8452540804 Q20 bases: 8142973031(96.3376%) Q30 bases: 7562470689(89.4698%) Filtering result: reads passed filter: 151097506 reads failed due to low quality: 1082948 reads failed due to too many N: 27398 reads failed due to too short: 1400908 reads with adapter trimmed: 56621166 bases trimmed due to adapters: 655781886 Duplication rate: 16.9417% Insert size peak (evaluated by paired-end reads): 20 JSON report: zr3534_2_R1.fastp-trim.20201130.report.json HTML report: zr3534_2_R1.fastp-trim.20201130.report.html /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 zr3534_2_R1.fq.gz --in2 zr3534_2_R2.fq.gz --detect_adapter_for_pe --detect_adapter_for_pe --trim_front1 10 --trim_front2 10 --thread 27 --html zr3534_2_R1.fastp-trim.20201130.report.html --json zr3534_2_R1.fastp-trim.20201130.report.json --out1 zr3534_2_R1.fastp-trim.20201130.fq.gz --out2 zr3534_2_R2.fastp-trim.20201130.fq.gz fastp v0.20.0, time used: 754 seconds Detecting adapter sequence for read1... No adapter detected for read1 Detecting adapter sequence for read2... No adapter detected for read2 WARNING: fastp uses up to 16 threads although you specified 27 Read1 before filtering: total reads: 79350310 total bases: 10102730658 Q20 bases: 9818403266(97.1856%) Q30 bases: 9239141714(91.4519%) Read2 before filtering: total reads: 79350310 total bases: 10096828009 Q20 bases: 9711705883(96.1857%) Q30 bases: 9026325955(89.3976%) Read1 after filtering: total reads: 78211968 total bases: 8859290435 Q20 bases: 8613716713(97.2281%) Q30 bases: 8093646007(91.3577%) Read2 aftering filtering: total reads: 78211968 total bases: 8851512811 Q20 bases: 8517428872(96.2257%) Q30 bases: 7897495240(89.222%) Filtering result: reads passed filter: 156423936 reads failed due to low quality: 937180 reads failed due to too many N: 28688 reads failed due to too short: 1310816 reads with adapter trimmed: 54468122 bases trimmed due to adapters: 624488399 Duplication rate: 16.6899% Insert size peak (evaluated by paired-end reads): 20 JSON report: zr3534_3_R1.fastp-trim.20201130.report.json HTML report: zr3534_3_R1.fastp-trim.20201130.report.html /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 zr3534_3_R1.fq.gz --in2 zr3534_3_R2.fq.gz --detect_adapter_for_pe --detect_adapter_for_pe --trim_front1 10 --trim_front2 10 --thread 27 --html zr3534_3_R1.fastp-trim.20201130.report.html --json zr3534_3_R1.fastp-trim.20201130.report.json --out1 zr3534_3_R1.fastp-trim.20201130.fq.gz --out2 zr3534_3_R2.fastp-trim.20201130.fq.gz fastp v0.20.0, time used: 798 seconds Detecting adapter sequence for read1... No adapter detected for read1 Detecting adapter sequence for read2... No adapter detected for read2 WARNING: fastp uses up to 16 threads although you specified 27 Read1 before filtering: total reads: 76075752 total bases: 9599918445 Q20 bases: 9237261273(96.2223%) Q30 bases: 8553721857(89.102%) Read2 before filtering: total reads: 76075752 total bases: 9596848791 Q20 bases: 9269463147(96.5886%) Q30 bases: 8661058380(90.249%) Read1 after filtering: total reads: 74862710 total bases: 8362530747 Q20 bases: 8051149831(96.2765%) Q30 bases: 7444392648(89.0208%) Read2 aftering filtering: total reads: 74862710 total bases: 8358528877 Q20 bases: 8077569678(96.6387%) Q30 bases: 7529795136(90.0852%) Filtering result: reads passed filter: 149725420 reads failed due to low quality: 900056 reads failed due to too many N: 24838 reads failed due to too short: 1501190 reads with adapter trimmed: 56895982 bases trimmed due to adapters: 659754161 Duplication rate: 16.6524% Insert size peak (evaluated by paired-end reads): 20 JSON report: zr3534_4_R1.fastp-trim.20201130.report.json HTML report: zr3534_4_R1.fastp-trim.20201130.report.html /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 zr3534_4_R1.fq.gz --in2 zr3534_4_R2.fq.gz --detect_adapter_for_pe --detect_adapter_for_pe --trim_front1 10 --trim_front2 10 --thread 27 --html zr3534_4_R1.fastp-trim.20201130.report.html --json zr3534_4_R1.fastp-trim.20201130.report.json --out1 zr3534_4_R1.fastp-trim.20201130.fq.gz --out2 zr3534_4_R2.fastp-trim.20201130.fq.gz fastp v0.20.0, time used: 820 seconds Detecting adapter sequence for read1... No adapter detected for read1 Detecting adapter sequence for read2... No adapter detected for read2 WARNING: fastp uses up to 16 threads although you specified 27 Read1 before filtering: total reads: 85730862 total bases: 10811602022 Q20 bases: 10506512436(97.1781%) Q30 bases: 9897436984(91.5446%) Read2 before filtering: total reads: 85730862 total bases: 10806775944 Q20 bases: 10390878028(96.1515%) Q30 bases: 9663380700(89.4196%) Read1 after filtering: total reads: 84202998 total bases: 9394622882 Q20 bases: 9141754730(97.3084%) Q30 bases: 8605342548(91.5986%) Read2 aftering filtering: total reads: 84202998 total bases: 9387046346 Q20 bases: 9033571043(96.2344%) Q30 bases: 8380693290(89.2793%) Filtering result: reads passed filter: 168405996 reads failed due to low quality: 1209448 reads failed due to too many N: 30256 reads failed due to too short: 1816024 reads with adapter trimmed: 64816960 bases trimmed due to adapters: 751519436 Duplication rate: 17.3446% Insert size peak (evaluated by paired-end reads): 20 JSON report: zr3534_5_R1.fastp-trim.20201130.report.json HTML report: zr3534_5_R1.fastp-trim.20201130.report.html /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 zr3534_5_R1.fq.gz --in2 zr3534_5_R2.fq.gz --detect_adapter_for_pe --detect_adapter_for_pe --trim_front1 10 --trim_front2 10 --thread 27 --html zr3534_5_R1.fastp-trim.20201130.report.html --json zr3534_5_R1.fastp-trim.20201130.report.json --out1 zr3534_5_R1.fastp-trim.20201130.fq.gz --out2 zr3534_5_R2.fastp-trim.20201130.fq.gz fastp v0.20.0, time used: 847 seconds Detecting adapter sequence for read1... No adapter detected for read1 Detecting adapter sequence for read2... No adapter detected for read2 WARNING: fastp uses up to 16 threads although you specified 27 Read1 before filtering: total reads: 76803843 total bases: 9727984064 Q20 bases: 9440947075(97.0494%) Q30 bases: 8886256058(91.3474%) Read2 before filtering: total reads: 76803843 total bases: 9724279046 Q20 bases: 9348544606(96.1361%) Q30 bases: 8691487697(89.3793%) Read1 after filtering: total reads: 75460315 total bases: 8481713419 Q20 bases: 8249680202(97.2643%) Q30 bases: 7757468112(91.4611%) Read2 aftering filtering: total reads: 75460315 total bases: 8475424299 Q20 bases: 8154608827(96.2148%) Q30 bases: 7562815975(89.2323%) Filtering result: reads passed filter: 150920630 reads failed due to low quality: 1927202 reads failed due to too many N: 26478 reads failed due to too short: 733376 reads with adapter trimmed: 54982602 bases trimmed due to adapters: 633345490 Duplication rate: 16.8533% Insert size peak (evaluated by paired-end reads): 20 JSON report: zr3534_6_R1.fastp-trim.20201130.report.json HTML report: zr3534_6_R1.fastp-trim.20201130.report.html /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 zr3534_6_R1.fq.gz --in2 zr3534_6_R2.fq.gz --detect_adapter_for_pe --detect_adapter_for_pe --trim_front1 10 --trim_front2 10 --thread 27 --html zr3534_6_R1.fastp-trim.20201130.report.html --json zr3534_6_R1.fastp-trim.20201130.report.json --out1 zr3534_6_R1.fastp-trim.20201130.fq.gz --out2 zr3534_6_R2.fastp-trim.20201130.fq.gz fastp v0.20.0, time used: 774 seconds Detecting adapter sequence for read1... No adapter detected for read1 Detecting adapter sequence for read2... No adapter detected for read2 WARNING: fastp uses up to 16 threads although you specified 27 Read1 before filtering: total reads: 67258007 total bases: 8500514440 Q20 bases: 8217743514(96.6735%) Q30 bases: 7669190900(90.2203%) Read2 before filtering: total reads: 67258007 total bases: 8496875250 Q20 bases: 8191869544(96.4104%) Q30 bases: 7639098871(89.9048%) Read1 after filtering: total reads: 66196742 total bases: 7415341319 Q20 bases: 7175358950(96.7637%) Q30 bases: 6688523227(90.1985%) Read2 aftering filtering: total reads: 66196742 total bases: 7410468063 Q20 bases: 7149899157(96.4838%) Q30 bases: 6651681317(89.7606%) Filtering result: reads passed filter: 132393484 reads failed due to low quality: 901570 reads failed due to too many N: 22642 reads failed due to too short: 1198318 reads with adapter trimmed: 49029346 bases trimmed due to adapters: 569389549 Duplication rate: 15.5437% Insert size peak (evaluated by paired-end reads): 20 JSON report: zr3534_7_R1.fastp-trim.20201130.report.json HTML report: zr3534_7_R1.fastp-trim.20201130.report.html /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 zr3534_7_R1.fq.gz --in2 zr3534_7_R2.fq.gz --detect_adapter_for_pe --detect_adapter_for_pe --trim_front1 10 --trim_front2 10 --thread 27 --html zr3534_7_R1.fastp-trim.20201130.report.html --json zr3534_7_R1.fastp-trim.20201130.report.json --out1 zr3534_7_R1.fastp-trim.20201130.fq.gz --out2 zr3534_7_R2.fastp-trim.20201130.fq.gz fastp v0.20.0, time used: 661 seconds Detecting adapter sequence for read1... No adapter detected for read1 Detecting adapter sequence for read2... No adapter detected for read2 WARNING: fastp uses up to 16 threads although you specified 27 Read1 before filtering: total reads: 92209405 total bases: 11585173243 Q20 bases: 10958451533(94.5903%) Q30 bases: 9906086700(85.5066%) Read2 before filtering: total reads: 92209405 total bases: 11581154841 Q20 bases: 11210505167(96.7995%) Q30 bases: 10494053858(90.6132%) Read1 after filtering: total reads: 90769971 total bases: 10063841208 Q20 bases: 9514735964(94.5438%) Q30 bases: 8582170864(85.2773%) Read2 aftering filtering: total reads: 90769971 total bases: 10061433510 Q20 bases: 9741980198(96.825%) Q30 bases: 9097265824(90.4172%) Filtering result: reads passed filter: 181539942 reads failed due to low quality: 1013150 reads failed due to too many N: 25522 reads failed due to too short: 1840196 reads with adapter trimmed: 72504992 bases trimmed due to adapters: 847388185 Duplication rate: 18.9507% Insert size peak (evaluated by paired-end reads): 20 JSON report: zr3534_8_R1.fastp-trim.20201130.report.json HTML report: zr3534_8_R1.fastp-trim.20201130.report.html /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 zr3534_8_R1.fq.gz --in2 zr3534_8_R2.fq.gz --detect_adapter_for_pe --detect_adapter_for_pe --trim_front1 10 --trim_front2 10 --thread 27 --html zr3534_8_R1.fastp-trim.20201130.report.html --json zr3534_8_R1.fastp-trim.20201130.report.json --out1 zr3534_8_R1.fastp-trim.20201130.fq.gz --out2 zr3534_8_R2.fastp-trim.20201130.fq.gz fastp v0.20.0, time used: 957 seconds Detecting adapter sequence for read1... No adapter detected for read1 Detecting adapter sequence for read2... No adapter detected for read2 WARNING: fastp uses up to 16 threads although you specified 27 Read1 before filtering: total reads: 75217875 total bases: 9487265913 Q20 bases: 9209615965(97.0734%) Q30 bases: 8652333619(91.1994%) Read2 before filtering: total reads: 75217875 total bases: 9484067486 Q20 bases: 9144507424(96.4197%) Q30 bases: 8531967189(89.9611%) Read1 after filtering: total reads: 73914588 total bases: 8247680640 Q20 bases: 8013279567(97.158%) Q30 bases: 7520644586(91.185%) Read2 aftering filtering: total reads: 73914588 total bases: 8242534635 Q20 bases: 7952349820(96.4794%) Q30 bases: 7402110001(89.8038%) Filtering result: reads passed filter: 147829176 reads failed due to low quality: 931938 reads failed due to too many N: 26098 reads failed due to too short: 1648538 reads with adapter trimmed: 56989326 bases trimmed due to adapters: 660029953 Duplication rate: 16.3912% Insert size peak (evaluated by paired-end reads): 20 JSON report: zr3534_9_R1.fastp-trim.20201130.report.json HTML report: zr3534_9_R1.fastp-trim.20201130.report.html /gscratch/srlab/programs/fastp-0.20.0/fastp --in1 zr3534_9_R1.fq.gz --in2 zr3534_9_R2.fq.gz --detect_adapter_for_pe --detect_adapter_for_pe --trim_front1 10 --trim_front2 10 --thread 27 --html zr3534_9_R1.fastp-trim.20201130.report.html --json zr3534_9_R1.fastp-trim.20201130.report.json --out1 zr3534_9_R1.fastp-trim.20201130.fq.gz --out2 zr3534_9_R2.fastp-trim.20201130.fq.gz fastp v0.20.0, time used: 724 seconds [INFO ] multiqc : This is MultiQC v1.8 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching : /gscratch/scrubbed/samwhite/outputs/20201130_cgig_fastp_ronit-ploidy-wgbs [INFO ] fastp : Found 10 reports [INFO ] multiqc : Compressing plot data [INFO ] multiqc : Report : multiqc_report.html [INFO ] multiqc : Data : multiqc_data [INFO ] multiqc : MultiQC complete