Mercurial > repos > iuc > mageck_pathway
diff test-data/out.test.log.txt @ 0:c871e57e2abb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 06:41:39 -0500 |
| parents | |
| children | ff3716b505d3 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.test.log.txt Wed Feb 14 06:41:39 2018 -0500 @@ -0,0 +1,112 @@ +INFO @ Mon, 12 Feb 2018 03:40:01: Parameters: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/bin/mageck test -k /tmp/tmp0xS0Jl/files/000/dataset_21.dat -t HL60.final,KBM7.final -c HL60.initial,KBM7.initial -n output --normcounts-to-file --pdf-report --norm-method median --gene-test-fdr-threshold 0.25 --adjust-method fdr --sort-criteria neg --remove-zero none --gene-lfc-method median +INFO @ Mon, 12 Feb 2018 03:40:01: Welcome to MAGeCK v0.5.7. Command: test +INFO @ Mon, 12 Feb 2018 03:40:01: Loading count table from /tmp/tmp0xS0Jl/files/000/dataset_21.dat +INFO @ Mon, 12 Feb 2018 03:40:01: Processing 1 lines.. +DEBUG @ Mon, 12 Feb 2018 03:40:01: Parsing error in line 1 (usually the header line). Skip this line. +INFO @ Mon, 12 Feb 2018 03:40:01: Loaded 999 records. +INFO @ Mon, 12 Feb 2018 03:40:01: Loading R template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template.RTemplate. +INFO @ Mon, 12 Feb 2018 03:40:01: Loading R template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template_indvgene.RTemplate. +INFO @ Mon, 12 Feb 2018 03:40:01: Loading Rnw template file: /home/maria/miniconda3/envs/mulled-v1-b1e6893952d2d7e4d51a13d040adcd7bea052bfdc57a24d59056014db875e749/lib/python3.6/site-packages/mageck/plot_template.Rnw. +DEBUG @ Mon, 12 Feb 2018 03:40:01: Setting up the visualization module... +DEBUG @ Mon, 12 Feb 2018 03:40:01: Given sample labels: HL60.final,KBM7.final +DEBUG @ Mon, 12 Feb 2018 03:40:01: Converted index: 2 3 +INFO @ Mon, 12 Feb 2018 03:40:01: Treatment samples:HL60.final,KBM7.final +INFO @ Mon, 12 Feb 2018 03:40:01: Treatment sample index:2,3 +DEBUG @ Mon, 12 Feb 2018 03:40:01: Given sample labels: HL60.initial,KBM7.initial +DEBUG @ Mon, 12 Feb 2018 03:40:01: Converted index: 0 1 +INFO @ Mon, 12 Feb 2018 03:40:01: Control samples:HL60.initial,KBM7.initial +INFO @ Mon, 12 Feb 2018 03:40:01: Control sample index:0,1 +DEBUG @ Mon, 12 Feb 2018 03:40:01: Initial (total) size factor: 1.6666455325878438 2.027372749328462 0.7198064117880387 0.6589869375844738 +DEBUG @ Mon, 12 Feb 2018 03:40:01: Median factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618 +INFO @ Mon, 12 Feb 2018 03:40:01: Final size factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618 +INFO @ Mon, 12 Feb 2018 03:40:01: Writing normalized read counts to output.normalized.txt +DEBUG @ Mon, 12 Feb 2018 03:40:01: Adjusted model: 1.1175084644498339 3.4299551007579927 +INFO @ Mon, 12 Feb 2018 03:40:01: Raw variance calculation: 0.5 for control, 0.5 for treatment +INFO @ Mon, 12 Feb 2018 03:40:01: Adjusted variance calculation: 0.3333333333333333 for raw variance, 0.6666666666666667 for modeling +INFO @ Mon, 12 Feb 2018 03:40:01: Use qnorm to reversely calculate sgRNA scores ... +DEBUG @ Mon, 12 Feb 2018 03:40:01: lower test FDR cutoff: 0.3283283283283283 +DEBUG @ Mon, 12 Feb 2018 03:40:01: higher test FDR cutoff: 0.34534534534534533 +INFO @ Mon, 12 Feb 2018 03:40:01: Running command: RRA -i output.plow.txt -o output.gene.low.txt -p 0.3283283283283283 --skip-gene NA --skip-gene na +INFO @ Mon, 12 Feb 2018 03:40:02: Command message: +INFO @ Mon, 12 Feb 2018 03:40:02: Welcome to RRA v 0.5.7. +INFO @ Mon, 12 Feb 2018 03:40:02: Skipping gene NA for permutation ... +INFO @ Mon, 12 Feb 2018 03:40:02: Skipping gene na for permutation ... +INFO @ Mon, 12 Feb 2018 03:40:02: Reading input file... +INFO @ Mon, 12 Feb 2018 03:40:02: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 +INFO @ Mon, 12 Feb 2018 03:40:02: Computing lo-values for each group... +INFO @ Mon, 12 Feb 2018 03:40:02: Computing false discovery rate... +INFO @ Mon, 12 Feb 2018 03:40:02: Increase the number of permutations to 1001 to get precise p values. To avoid this, use the --permutation option. +INFO @ Mon, 12 Feb 2018 03:40:02: Permuting genes with 9 sgRNAs... +INFO @ Mon, 12 Feb 2018 03:40:02: Permuting genes with 10 sgRNAs... +INFO @ Mon, 12 Feb 2018 03:40:02: Number of genes under FDR adjustment: 100 +INFO @ Mon, 12 Feb 2018 03:40:02: Saving to output file... +INFO @ Mon, 12 Feb 2018 03:40:02: RRA completed. +INFO @ Mon, 12 Feb 2018 03:40:02: +INFO @ Mon, 12 Feb 2018 03:40:02: End command message. +INFO @ Mon, 12 Feb 2018 03:40:02: Running command: RRA -i output.phigh.txt -o output.gene.high.txt -p 0.34534534534534533 --skip-gene NA --skip-gene na +INFO @ Mon, 12 Feb 2018 03:40:03: Command message: +INFO @ Mon, 12 Feb 2018 03:40:03: Welcome to RRA v 0.5.7. +INFO @ Mon, 12 Feb 2018 03:40:03: Skipping gene NA for permutation ... +INFO @ Mon, 12 Feb 2018 03:40:03: Skipping gene na for permutation ... +INFO @ Mon, 12 Feb 2018 03:40:03: Reading input file... +INFO @ Mon, 12 Feb 2018 03:40:03: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 +INFO @ Mon, 12 Feb 2018 03:40:03: Computing lo-values for each group... +INFO @ Mon, 12 Feb 2018 03:40:03: Computing false discovery rate... +INFO @ Mon, 12 Feb 2018 03:40:03: Increase the number of permutations to 1001 to get precise p values. To avoid this, use the --permutation option. +INFO @ Mon, 12 Feb 2018 03:40:03: Permuting genes with 9 sgRNAs... +INFO @ Mon, 12 Feb 2018 03:40:03: Permuting genes with 10 sgRNAs... +INFO @ Mon, 12 Feb 2018 03:40:03: Number of genes under FDR adjustment: 100 +INFO @ Mon, 12 Feb 2018 03:40:03: Saving to output file... +INFO @ Mon, 12 Feb 2018 03:40:03: RRA completed. +INFO @ Mon, 12 Feb 2018 03:40:03: +INFO @ Mon, 12 Feb 2018 03:40:03: End command message. +DEBUG @ Mon, 12 Feb 2018 03:40:03: Sorting the merged items by negative selection... +INFO @ Mon, 12 Feb 2018 03:40:03: Loading top 10 genes from output.gene.low.txt: ACIN1,ACTR8,AHCY,ACLY,AATF,AGBL5,AHCTF1,ABT1,ADIRF,ABCF1 +DEBUG @ Mon, 12 Feb 2018 03:40:03: Column index:3 +INFO @ Mon, 12 Feb 2018 03:40:03: Loading top 10 genes from output.gene.high.txt: ACRC,AGAP3,ADCK4,AHRR,ADRBK1,ADK,ADCK1,ADARB2,ACSS2,ADNP +DEBUG @ Mon, 12 Feb 2018 03:40:03: Column index:9 +INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.plow.txt +INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.phigh.txt +INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.gene.low.txt +INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.gene.high.txt +INFO @ Mon, 12 Feb 2018 03:40:03: Running command: cd ./; Rscript output.R +INFO @ Mon, 12 Feb 2018 03:40:04: Command message: +INFO @ Mon, 12 Feb 2018 03:40:04: null device +INFO @ Mon, 12 Feb 2018 03:40:04: 1 +INFO @ Mon, 12 Feb 2018 03:40:04: Writing to file output_summary.tex +INFO @ Mon, 12 Feb 2018 03:40:04: Processing code chunks with options ... +INFO @ Mon, 12 Feb 2018 03:40:04: 1 : keep.source term verbatim (label = funcdef, output_summary.Rnw:27) +INFO @ Mon, 12 Feb 2018 03:40:04: 2 : keep.source term tex (label = tab1, output_summary.Rnw:37) +INFO @ Mon, 12 Feb 2018 03:40:04: 3 : keep.source term verbatim (output_summary.Rnw:77) +INFO @ Mon, 12 Feb 2018 03:40:04: 4 : keep.source term verbatim pdf (output_summary.Rnw:83) +INFO @ Mon, 12 Feb 2018 03:40:04: 5 : keep.source term verbatim pdf (output_summary.Rnw:201) +INFO @ Mon, 12 Feb 2018 03:40:04: 6 : keep.source term verbatim pdf (output_summary.Rnw:345) +INFO @ Mon, 12 Feb 2018 03:40:04: 7 : keep.source term verbatim pdf (output_summary.Rnw:489) +INFO @ Mon, 12 Feb 2018 03:40:04: 8 : keep.source term verbatim (output_summary.Rnw:567) +INFO @ Mon, 12 Feb 2018 03:40:04: 9 : keep.source term verbatim pdf (output_summary.Rnw:573) +INFO @ Mon, 12 Feb 2018 03:40:04: 10 : keep.source term verbatim pdf (output_summary.Rnw:691) +INFO @ Mon, 12 Feb 2018 03:40:04: 11 : keep.source term verbatim pdf (output_summary.Rnw:835) +INFO @ Mon, 12 Feb 2018 03:40:04: 12 : keep.source term verbatim pdf (output_summary.Rnw:979) +INFO @ Mon, 12 Feb 2018 03:40:04: +INFO @ Mon, 12 Feb 2018 03:40:04: You can now run (pdf)latex on ‘output_summary.tex’ +INFO @ Mon, 12 Feb 2018 03:40:04: Error in texi2dvi("output_summary.tex", pdf = TRUE) : +INFO @ Mon, 12 Feb 2018 03:40:04: pdflatex is not available +INFO @ Mon, 12 Feb 2018 03:40:04: Execution halted +INFO @ Mon, 12 Feb 2018 03:40:04: +INFO @ Mon, 12 Feb 2018 03:40:04: End command message. +INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary-*.pdf +INFO @ Mon, 12 Feb 2018 03:40:04: Command message: +INFO @ Mon, 12 Feb 2018 03:40:04: +INFO @ Mon, 12 Feb 2018 03:40:04: End command message. +INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.aux +INFO @ Mon, 12 Feb 2018 03:40:04: Command message: +INFO @ Mon, 12 Feb 2018 03:40:04: +INFO @ Mon, 12 Feb 2018 03:40:04: End command message. +INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.tex +INFO @ Mon, 12 Feb 2018 03:40:04: Command message: +INFO @ Mon, 12 Feb 2018 03:40:04: +INFO @ Mon, 12 Feb 2018 03:40:04: End command message. +INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.toc +INFO @ Mon, 12 Feb 2018 03:40:04: Command message: +INFO @ Mon, 12 Feb 2018 03:40:04: +INFO @ Mon, 12 Feb 2018 03:40:04: End command message.