Mercurial > repos > iuc > mageck_gsea
view test-data/out.test.log.txt @ 3:f259c29b3832 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
| author | iuc |
|---|---|
| date | Thu, 19 Apr 2018 05:34:15 -0400 |
| parents | 82a180e6b582 |
| children |
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INFO @ Mon, 26 Mar 2018 08:37:53: Parameters: /Users/doylemaria/miniconda3/envs/mulled-v1-9ee130591ca78526e74a59d8d6dc03cb7db20645470975762936caeac62972dc/bin/mageck test -k /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpTX65kA/files/000/dataset_4.dat -t HL60_final,KBM7_final -c HL60_initial,KBM7_initial -n output --normcounts-to-file --pdf-report --norm-method median --adjust-method fdr --sort-criteria neg --remove-zero both --gene-lfc-method median INFO @ Mon, 26 Mar 2018 08:37:53: Welcome to MAGeCK v0.5.7. Command: test INFO @ Mon, 26 Mar 2018 08:37:53: Loading count table from /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpTX65kA/files/000/dataset_4.dat INFO @ Mon, 26 Mar 2018 08:37:53: Processing 1 lines.. DEBUG @ Mon, 26 Mar 2018 08:37:53: Parsing error in line 1 (usually the header line). Skip this line. INFO @ Mon, 26 Mar 2018 08:37:53: Loaded 999 records. INFO @ Mon, 26 Mar 2018 08:37:53: Loading R template file: /Users/doylemaria/miniconda3/envs/mulled-v1-9ee130591ca78526e74a59d8d6dc03cb7db20645470975762936caeac62972dc/lib/python3.6/site-packages/mageck/plot_template.RTemplate. INFO @ Mon, 26 Mar 2018 08:37:53: Loading R template file: /Users/doylemaria/miniconda3/envs/mulled-v1-9ee130591ca78526e74a59d8d6dc03cb7db20645470975762936caeac62972dc/lib/python3.6/site-packages/mageck/plot_template_indvgene.RTemplate. INFO @ Mon, 26 Mar 2018 08:37:53: Loading Rnw template file: /Users/doylemaria/miniconda3/envs/mulled-v1-9ee130591ca78526e74a59d8d6dc03cb7db20645470975762936caeac62972dc/lib/python3.6/site-packages/mageck/plot_template.Rnw. DEBUG @ Mon, 26 Mar 2018 08:37:53: Setting up the visualization module... DEBUG @ Mon, 26 Mar 2018 08:37:53: Given sample labels: HL60_final,KBM7_final DEBUG @ Mon, 26 Mar 2018 08:37:53: Converted index: 2 3 INFO @ Mon, 26 Mar 2018 08:37:53: Treatment samples:HL60_final,KBM7_final INFO @ Mon, 26 Mar 2018 08:37:53: Treatment sample index:2,3 DEBUG @ Mon, 26 Mar 2018 08:37:53: Given sample labels: HL60_initial,KBM7_initial DEBUG @ Mon, 26 Mar 2018 08:37:53: Converted index: 0 1 INFO @ Mon, 26 Mar 2018 08:37:53: Control samples:HL60_initial,KBM7_initial INFO @ Mon, 26 Mar 2018 08:37:53: Control sample index:0,1 DEBUG @ Mon, 26 Mar 2018 08:37:53: Initial (total) size factor: 1.6666455325878438 2.027372749328462 0.7198064117880387 0.6589869375844738 DEBUG @ Mon, 26 Mar 2018 08:37:53: Median factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618 INFO @ Mon, 26 Mar 2018 08:37:53: Final size factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618 INFO @ Mon, 26 Mar 2018 08:37:53: Writing normalized read counts to output.normalized.txt DEBUG @ Mon, 26 Mar 2018 08:37:53: Adjusted model: 1.1175084644498339 3.4299551007579927 INFO @ Mon, 26 Mar 2018 08:37:53: Raw variance calculation: 0.5 for control, 0.5 for treatment INFO @ Mon, 26 Mar 2018 08:37:53: Adjusted variance calculation: 0.3333333333333333 for raw variance, 0.6666666666666667 for modeling INFO @ Mon, 26 Mar 2018 08:37:53: Use qnorm to reversely calculate sgRNA scores ... DEBUG @ Mon, 26 Mar 2018 08:37:53: lower test FDR cutoff: 0.3283283283283283 DEBUG @ Mon, 26 Mar 2018 08:37:53: higher test FDR cutoff: 0.34534534534534533 INFO @ Mon, 26 Mar 2018 08:37:53: Running command: RRA -i output.plow.txt -o output.gene.low.txt -p 0.3283283283283283 --skip-gene NA --skip-gene na INFO @ Mon, 26 Mar 2018 08:37:53: Command message: INFO @ Mon, 26 Mar 2018 08:37:53: Welcome to RRA v 0.5.7. INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene NA for permutation ... INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene na for permutation ... INFO @ Mon, 26 Mar 2018 08:37:53: Reading input file... INFO @ Mon, 26 Mar 2018 08:37:53: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 INFO @ Mon, 26 Mar 2018 08:37:53: Computing lo-values for each group... INFO @ Mon, 26 Mar 2018 08:37:53: Computing false discovery rate... INFO @ Mon, 26 Mar 2018 08:37:53: Increase the number of permutations to 1001 to get precise p values. To avoid this, use the --permutation option. INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 9 sgRNAs... INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 10 sgRNAs... INFO @ Mon, 26 Mar 2018 08:37:53: Number of genes under FDR adjustment: 100 INFO @ Mon, 26 Mar 2018 08:37:53: Saving to output file... INFO @ Mon, 26 Mar 2018 08:37:53: RRA completed. INFO @ Mon, 26 Mar 2018 08:37:53: INFO @ Mon, 26 Mar 2018 08:37:53: End command message. INFO @ Mon, 26 Mar 2018 08:37:53: Running command: RRA -i output.phigh.txt -o output.gene.high.txt -p 0.34534534534534533 --skip-gene NA --skip-gene na INFO @ Mon, 26 Mar 2018 08:37:53: Command message: INFO @ Mon, 26 Mar 2018 08:37:53: Welcome to RRA v 0.5.7. INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene NA for permutation ... INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene na for permutation ... INFO @ Mon, 26 Mar 2018 08:37:53: Reading input file... INFO @ Mon, 26 Mar 2018 08:37:53: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 INFO @ Mon, 26 Mar 2018 08:37:53: Computing lo-values for each group... INFO @ Mon, 26 Mar 2018 08:37:53: Computing false discovery rate... INFO @ Mon, 26 Mar 2018 08:37:53: Increase the number of permutations to 1001 to get precise p values. To avoid this, use the --permutation option. INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 9 sgRNAs... INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 10 sgRNAs... INFO @ Mon, 26 Mar 2018 08:37:53: Number of genes under FDR adjustment: 100 INFO @ Mon, 26 Mar 2018 08:37:53: Saving to output file... INFO @ Mon, 26 Mar 2018 08:37:53: RRA completed. INFO @ Mon, 26 Mar 2018 08:37:53: INFO @ Mon, 26 Mar 2018 08:37:53: End command message. DEBUG @ Mon, 26 Mar 2018 08:37:53: Sorting the merged items by negative selection... INFO @ Mon, 26 Mar 2018 08:37:53: Loading top 10 genes from output.gene.low.txt: ACIN1,ACTR8,AHCY,ACLY,AATF,AGBL5,AHCTF1,ABT1,ADIRF,ABCF1 DEBUG @ Mon, 26 Mar 2018 08:37:53: Column index:3 INFO @ Mon, 26 Mar 2018 08:37:53: Loading top 10 genes from output.gene.high.txt: ACRC,AGAP3,ADCK4,AHRR,ADRBK1,ADK,ADCK1,ADARB2,ACSS2,ADNP DEBUG @ Mon, 26 Mar 2018 08:37:53: Column index:9 INFO @ Mon, 26 Mar 2018 08:37:53: Running command: rm output.plow.txt INFO @ Mon, 26 Mar 2018 08:37:53: Running command: rm output.phigh.txt INFO @ Mon, 26 Mar 2018 08:37:54: Running command: rm output.gene.low.txt INFO @ Mon, 26 Mar 2018 08:37:54: Running command: rm output.gene.high.txt INFO @ Mon, 26 Mar 2018 08:37:54: Running command: cd ./; Rscript output.R INFO @ Mon, 26 Mar 2018 08:37:59: Command message: INFO @ Mon, 26 Mar 2018 08:37:59: null device INFO @ Mon, 26 Mar 2018 08:37:59: 1 INFO @ Mon, 26 Mar 2018 08:37:59: Writing to file output_summary.tex INFO @ Mon, 26 Mar 2018 08:37:59: Processing code chunks with options ... INFO @ Mon, 26 Mar 2018 08:37:59: 1 : keep.source term verbatim (label = funcdef, output_summary.Rnw:27) INFO @ Mon, 26 Mar 2018 08:37:59: 2 : keep.source term tex (label = tab1, output_summary.Rnw:37) INFO @ Mon, 26 Mar 2018 08:37:59: 3 : keep.source term verbatim (output_summary.Rnw:77) INFO @ Mon, 26 Mar 2018 08:37:59: 4 : keep.source term verbatim pdf (output_summary.Rnw:83) INFO @ Mon, 26 Mar 2018 08:37:59: 5 : keep.source term verbatim pdf (output_summary.Rnw:201) INFO @ Mon, 26 Mar 2018 08:37:59: 6 : keep.source term verbatim pdf (output_summary.Rnw:345) INFO @ Mon, 26 Mar 2018 08:37:59: 7 : keep.source term verbatim pdf (output_summary.Rnw:489) INFO @ Mon, 26 Mar 2018 08:37:59: 8 : keep.source term verbatim (output_summary.Rnw:567) INFO @ Mon, 26 Mar 2018 08:37:59: 9 : keep.source term verbatim pdf (output_summary.Rnw:573) INFO @ Mon, 26 Mar 2018 08:37:59: 10 : keep.source term verbatim pdf (output_summary.Rnw:691) INFO @ Mon, 26 Mar 2018 08:37:59: 11 : keep.source term verbatim pdf (output_summary.Rnw:835) INFO @ Mon, 26 Mar 2018 08:37:59: 12 : keep.source term verbatim pdf (output_summary.Rnw:979) INFO @ Mon, 26 Mar 2018 08:37:59: INFO @ Mon, 26 Mar 2018 08:37:59: You can now run (pdf)latex on ‘output_summary.tex’ INFO @ Mon, 26 Mar 2018 08:37:59: INFO @ Mon, 26 Mar 2018 08:37:59: End command message. INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary-*.pdf INFO @ Mon, 26 Mar 2018 08:37:59: Command message: INFO @ Mon, 26 Mar 2018 08:37:59: INFO @ Mon, 26 Mar 2018 08:37:59: End command message. INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary.aux INFO @ Mon, 26 Mar 2018 08:37:59: Command message: INFO @ Mon, 26 Mar 2018 08:37:59: INFO @ Mon, 26 Mar 2018 08:37:59: End command message. INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary.tex INFO @ Mon, 26 Mar 2018 08:37:59: Command message: INFO @ Mon, 26 Mar 2018 08:37:59: INFO @ Mon, 26 Mar 2018 08:37:59: End command message. INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary.toc INFO @ Mon, 26 Mar 2018 08:37:59: Command message: INFO @ Mon, 26 Mar 2018 08:37:59: INFO @ Mon, 26 Mar 2018 08:37:59: End command message.