Open HenrikBengtsson opened 2 years ago
Comparing lg3 2021-10-11 Patient157t10 results to those of lg3 2021-10-08 gives:
[henrik@c4-dev3 test-2021-10-11]$ LG3_TEST_TRUTH=../test-2021-10-08/truth PATIENT=Patient157t10 lg3 test validate Sourced: /c4/home/henrik/repositories/UCSF-CostelloLab/LG3_Pipeline/lg3.conf Located: ./lg3.conf [PWD=/c4/home/henrik/repositories/UCSF-CostelloLab/test-next-release] Sourced: /c4/home/henrik/repositories/UCSF-CostelloLab/test-next-release/lg3.conf (55 bytes) *** Configuration [OK] PROJECT=LG3 [OK] PATIENT=Patient157t10 [OK] CONV=patient_ID_conversions.tsv [OK] LG3_TEST_TRUTH=../test-2021-10-08/truth *** Trimming of FASTQ Files [OK] file tree ('output/LG3/trim/Z00*-trim') [WARN] unexpected file sizes ('../test-2021-10-08/truth/Patient157t10/output/LG3/trim/Z00*-trim/*' != 'output/LG3/trim/Z00*-trim/*') @@ -2 +2 @@ -1725 output/LG3/trim/Z00599t10-trim/Z00599t10-trim_R1.trimming_report.txt +1743 output/LG3/trim/Z00599t10-trim/Z00599t10-trim_R1.trimming_report.txt @@ -4 +4 @@ -1987 output/LG3/trim/Z00599t10-trim/Z00599t10-trim_R2.trimming_report.txt +2005 output/LG3/trim/Z00599t10-trim/Z00599t10-trim_R2.trimming_report.txt @@ -6 +6 @@ -1747 output/LG3/trim/Z00600t10-trim/Z00600t10-trim_R1.trimming_report.txt +1765 output/LG3/trim/Z00600t10-trim/Z00600t10-trim_R1.trimming_report.txt @@ -8 +8 @@ -1934 output/LG3/trim/Z00600t10-trim/Z00600t10-trim_R2.trimming_report.txt +1952 output/LG3/trim/Z00600t10-trim/Z00600t10-trim_R2.trimming_report.txt @@ -10 +10 @@ -1769 output/LG3/trim/Z00601t10-trim/Z00601t10-trim_R1.trimming_report.txt +1787 output/LG3/trim/Z00601t10-trim/Z00601t10-trim_R1.trimming_report.txt @@ -12 +12 @@ -1954 output/LG3/trim/Z00601t10-trim/Z00601t10-trim_R2.trimming_report.txt +1972 output/LG3/trim/Z00601t10-trim/Z00601t10-trim_R2.trimming_report.txt [WARN] unexpected file md5 checksums (after gunzip) ('../test-2021-10-08/truth/Patient157t10/output/LG3/trim/Z00*-trim/*.fastq.gz' != 'output/LG3/trim/Z00*-trim/*.fastq.gz') *** BWA Alignment of FASTQ Files [OK] file tree ('output/LG3/exomes') [OK] file sizes ('output/LG3/exomes/Z00*/*') [OK] file md5 checksums ('output/LG3/exomes/Z00*/*.bai') [OK] file md5 checksums ('output/LG3/exomes/Z00*/*.bam') [OK] file md5 checksums ('output/LG3/exomes/Z00*/*.flagstat') *** Recalibration of BAM Files [OK] file tree ('output/LG3/exomes_recal/Patient157t10') [OK] file sizes ('output/LG3/exomes_recal/Patient157t10/*') [OK] file sizes ('output/LG3/exomes_recal/Patient157t10/germline/*') [OK] file md5 checksums ('output/LG3/exomes_recal/Patient157t10/germline/*.germline') [OK] file sizes ('output/LG3/exomes_recal/Patient157t10/*.bai') [OK] file md5 checksums ('output/LG3/exomes_recal/Patient157t10/*.flagstat') [OK] file md5 checksums ('output/LG3/exomes_recal/Patient157t10/*.bai') [OK] file md5 checksums ('output/LG3/exomes_recal/Patient157t10/*.bam') *** Pindel Processing [OK] file tree ('output/LG3/pindel') [OK] file rows ('output/LG3/pindel/Patient157t10.pindel.cfg') [OK] file sizes ('output/LG3/pindel/Patient157t10_pindel/*') [OK] file md5 checksums ('output/LG3/pindel/Patient157t10_pindel/*') *** MutDet Processing [OK] file tree ('output/LG3/mutations/Patient157t10_mutect') [OK] file sizes ('output/LG3/mutations/Patient157t10_mutect/*') [OK] file md5 checksums ('output/LG3/mutations/Patient157t10_mutect/*.mutations') [OK] file md5 checksums ('output/LG3/mutations/Patient157t10_mutect/*.txt') [OK] file md5 checksums ('output/LG3/mutations/Patient157t10_mutect/*.intersect.bed') *** Post-MutDet Processing [OK] file tree ('output/LG3/MAF') [OK] file sizes ('output/LG3/MAF/Patient157t10_MAF/*') [WARN] unexpected file sizes ('../test-2021-10-08/truth/Patient157t10/output/LG3/MAF/Patient157t10_plots/*' != 'output/LG3/MAF/Patient157t10_plots/*') @@ -1,4 +1,4 @@ -32K output/LG3/MAF/Patient157t10_plots/Patient157t10.LOH.chr17.pdf -41K output/LG3/MAF/Patient157t10_plots/Patient157t10.LOH.chr19.pdf -41K output/LG3/MAF/Patient157t10_plots/Patient157t10.LOH.grid.chr17.pdf -54K output/LG3/MAF/Patient157t10_plots/Patient157t10.LOH.grid.chr19.pdf +267K output/LG3/MAF/Patient157t10_plots/Patient157t10.LOH.chr17.pdf +365K output/LG3/MAF/Patient157t10_plots/Patient157t10.LOH.chr19.pdf +364K output/LG3/MAF/Patient157t10_plots/Patient157t10.LOH.grid.chr17.pdf +498K output/LG3/MAF/Patient157t10_plots/Patient157t10.LOH.grid.chr19.pdf [OK] file tree ('output/LG3/MutInDel') [OK] file sizes ('output/LG3/MutInDel/*') [OK] file content ('output/LG3/MutInDel/Patient157t10.R.mutations') [henrik@c4-dev3 test-2021-10-11]$
Comparing lg3 2021-10-11 Patient157t10 results to those of lg3 2021-10-08 gives: