Mercurial > repos > iuc > mageck_mle
comparison test-data/out.test.log.txt @ 0:eab37e8fea75 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 06:42:36 -0500 |
| parents | |
| children | 9cd937788131 |
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| -1:000000000000 | 0:eab37e8fea75 |
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| 1 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 | |
| 2 INFO @ Mon, 12 Feb 2018 03:40:01: Welcome to MAGeCK v0.5.7. Command: test | |
| 3 INFO @ Mon, 12 Feb 2018 03:40:01: Loading count table from /tmp/tmp0xS0Jl/files/000/dataset_21.dat | |
| 4 INFO @ Mon, 12 Feb 2018 03:40:01: Processing 1 lines.. | |
| 5 DEBUG @ Mon, 12 Feb 2018 03:40:01: Parsing error in line 1 (usually the header line). Skip this line. | |
| 6 INFO @ Mon, 12 Feb 2018 03:40:01: Loaded 999 records. | |
| 7 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. | |
| 8 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. | |
| 9 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. | |
| 10 DEBUG @ Mon, 12 Feb 2018 03:40:01: Setting up the visualization module... | |
| 11 DEBUG @ Mon, 12 Feb 2018 03:40:01: Given sample labels: HL60.final,KBM7.final | |
| 12 DEBUG @ Mon, 12 Feb 2018 03:40:01: Converted index: 2 3 | |
| 13 INFO @ Mon, 12 Feb 2018 03:40:01: Treatment samples:HL60.final,KBM7.final | |
| 14 INFO @ Mon, 12 Feb 2018 03:40:01: Treatment sample index:2,3 | |
| 15 DEBUG @ Mon, 12 Feb 2018 03:40:01: Given sample labels: HL60.initial,KBM7.initial | |
| 16 DEBUG @ Mon, 12 Feb 2018 03:40:01: Converted index: 0 1 | |
| 17 INFO @ Mon, 12 Feb 2018 03:40:01: Control samples:HL60.initial,KBM7.initial | |
| 18 INFO @ Mon, 12 Feb 2018 03:40:01: Control sample index:0,1 | |
| 19 DEBUG @ Mon, 12 Feb 2018 03:40:01: Initial (total) size factor: 1.6666455325878438 2.027372749328462 0.7198064117880387 0.6589869375844738 | |
| 20 DEBUG @ Mon, 12 Feb 2018 03:40:01: Median factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618 | |
| 21 INFO @ Mon, 12 Feb 2018 03:40:01: Final size factor: 1.469870985815957 1.7759474888175155 0.6308897693810006 0.5721813161032618 | |
| 22 INFO @ Mon, 12 Feb 2018 03:40:01: Writing normalized read counts to output.normalized.txt | |
| 23 DEBUG @ Mon, 12 Feb 2018 03:40:01: Adjusted model: 1.1175084644498339 3.4299551007579927 | |
| 24 INFO @ Mon, 12 Feb 2018 03:40:01: Raw variance calculation: 0.5 for control, 0.5 for treatment | |
| 25 INFO @ Mon, 12 Feb 2018 03:40:01: Adjusted variance calculation: 0.3333333333333333 for raw variance, 0.6666666666666667 for modeling | |
| 26 INFO @ Mon, 12 Feb 2018 03:40:01: Use qnorm to reversely calculate sgRNA scores ... | |
| 27 DEBUG @ Mon, 12 Feb 2018 03:40:01: lower test FDR cutoff: 0.3283283283283283 | |
| 28 DEBUG @ Mon, 12 Feb 2018 03:40:01: higher test FDR cutoff: 0.34534534534534533 | |
| 29 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 | |
| 30 INFO @ Mon, 12 Feb 2018 03:40:02: Command message: | |
| 31 INFO @ Mon, 12 Feb 2018 03:40:02: Welcome to RRA v 0.5.7. | |
| 32 INFO @ Mon, 12 Feb 2018 03:40:02: Skipping gene NA for permutation ... | |
| 33 INFO @ Mon, 12 Feb 2018 03:40:02: Skipping gene na for permutation ... | |
| 34 INFO @ Mon, 12 Feb 2018 03:40:02: Reading input file... | |
| 35 INFO @ Mon, 12 Feb 2018 03:40:02: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 | |
| 36 INFO @ Mon, 12 Feb 2018 03:40:02: Computing lo-values for each group... | |
| 37 INFO @ Mon, 12 Feb 2018 03:40:02: Computing false discovery rate... | |
| 38 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. | |
| 39 INFO @ Mon, 12 Feb 2018 03:40:02: Permuting genes with 9 sgRNAs... | |
| 40 INFO @ Mon, 12 Feb 2018 03:40:02: Permuting genes with 10 sgRNAs... | |
| 41 INFO @ Mon, 12 Feb 2018 03:40:02: Number of genes under FDR adjustment: 100 | |
| 42 INFO @ Mon, 12 Feb 2018 03:40:02: Saving to output file... | |
| 43 INFO @ Mon, 12 Feb 2018 03:40:02: RRA completed. | |
| 44 INFO @ Mon, 12 Feb 2018 03:40:02: | |
| 45 INFO @ Mon, 12 Feb 2018 03:40:02: End command message. | |
| 46 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 | |
| 47 INFO @ Mon, 12 Feb 2018 03:40:03: Command message: | |
| 48 INFO @ Mon, 12 Feb 2018 03:40:03: Welcome to RRA v 0.5.7. | |
| 49 INFO @ Mon, 12 Feb 2018 03:40:03: Skipping gene NA for permutation ... | |
| 50 INFO @ Mon, 12 Feb 2018 03:40:03: Skipping gene na for permutation ... | |
| 51 INFO @ Mon, 12 Feb 2018 03:40:03: Reading input file... | |
| 52 INFO @ Mon, 12 Feb 2018 03:40:03: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 | |
| 53 INFO @ Mon, 12 Feb 2018 03:40:03: Computing lo-values for each group... | |
| 54 INFO @ Mon, 12 Feb 2018 03:40:03: Computing false discovery rate... | |
| 55 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. | |
| 56 INFO @ Mon, 12 Feb 2018 03:40:03: Permuting genes with 9 sgRNAs... | |
| 57 INFO @ Mon, 12 Feb 2018 03:40:03: Permuting genes with 10 sgRNAs... | |
| 58 INFO @ Mon, 12 Feb 2018 03:40:03: Number of genes under FDR adjustment: 100 | |
| 59 INFO @ Mon, 12 Feb 2018 03:40:03: Saving to output file... | |
| 60 INFO @ Mon, 12 Feb 2018 03:40:03: RRA completed. | |
| 61 INFO @ Mon, 12 Feb 2018 03:40:03: | |
| 62 INFO @ Mon, 12 Feb 2018 03:40:03: End command message. | |
| 63 DEBUG @ Mon, 12 Feb 2018 03:40:03: Sorting the merged items by negative selection... | |
| 64 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 | |
| 65 DEBUG @ Mon, 12 Feb 2018 03:40:03: Column index:3 | |
| 66 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 | |
| 67 DEBUG @ Mon, 12 Feb 2018 03:40:03: Column index:9 | |
| 68 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.plow.txt | |
| 69 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.phigh.txt | |
| 70 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.gene.low.txt | |
| 71 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.gene.high.txt | |
| 72 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: cd ./; Rscript output.R | |
| 73 INFO @ Mon, 12 Feb 2018 03:40:04: Command message: | |
| 74 INFO @ Mon, 12 Feb 2018 03:40:04: null device | |
| 75 INFO @ Mon, 12 Feb 2018 03:40:04: 1 | |
| 76 INFO @ Mon, 12 Feb 2018 03:40:04: Writing to file output_summary.tex | |
| 77 INFO @ Mon, 12 Feb 2018 03:40:04: Processing code chunks with options ... | |
| 78 INFO @ Mon, 12 Feb 2018 03:40:04: 1 : keep.source term verbatim (label = funcdef, output_summary.Rnw:27) | |
| 79 INFO @ Mon, 12 Feb 2018 03:40:04: 2 : keep.source term tex (label = tab1, output_summary.Rnw:37) | |
| 80 INFO @ Mon, 12 Feb 2018 03:40:04: 3 : keep.source term verbatim (output_summary.Rnw:77) | |
| 81 INFO @ Mon, 12 Feb 2018 03:40:04: 4 : keep.source term verbatim pdf (output_summary.Rnw:83) | |
| 82 INFO @ Mon, 12 Feb 2018 03:40:04: 5 : keep.source term verbatim pdf (output_summary.Rnw:201) | |
| 83 INFO @ Mon, 12 Feb 2018 03:40:04: 6 : keep.source term verbatim pdf (output_summary.Rnw:345) | |
| 84 INFO @ Mon, 12 Feb 2018 03:40:04: 7 : keep.source term verbatim pdf (output_summary.Rnw:489) | |
| 85 INFO @ Mon, 12 Feb 2018 03:40:04: 8 : keep.source term verbatim (output_summary.Rnw:567) | |
| 86 INFO @ Mon, 12 Feb 2018 03:40:04: 9 : keep.source term verbatim pdf (output_summary.Rnw:573) | |
| 87 INFO @ Mon, 12 Feb 2018 03:40:04: 10 : keep.source term verbatim pdf (output_summary.Rnw:691) | |
| 88 INFO @ Mon, 12 Feb 2018 03:40:04: 11 : keep.source term verbatim pdf (output_summary.Rnw:835) | |
| 89 INFO @ Mon, 12 Feb 2018 03:40:04: 12 : keep.source term verbatim pdf (output_summary.Rnw:979) | |
| 90 INFO @ Mon, 12 Feb 2018 03:40:04: | |
| 91 INFO @ Mon, 12 Feb 2018 03:40:04: You can now run (pdf)latex on ‘output_summary.tex’ | |
| 92 INFO @ Mon, 12 Feb 2018 03:40:04: Error in texi2dvi("output_summary.tex", pdf = TRUE) : | |
| 93 INFO @ Mon, 12 Feb 2018 03:40:04: pdflatex is not available | |
| 94 INFO @ Mon, 12 Feb 2018 03:40:04: Execution halted | |
| 95 INFO @ Mon, 12 Feb 2018 03:40:04: | |
| 96 INFO @ Mon, 12 Feb 2018 03:40:04: End command message. | |
| 97 INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary-*.pdf | |
| 98 INFO @ Mon, 12 Feb 2018 03:40:04: Command message: | |
| 99 INFO @ Mon, 12 Feb 2018 03:40:04: | |
| 100 INFO @ Mon, 12 Feb 2018 03:40:04: End command message. | |
| 101 INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.aux | |
| 102 INFO @ Mon, 12 Feb 2018 03:40:04: Command message: | |
| 103 INFO @ Mon, 12 Feb 2018 03:40:04: | |
| 104 INFO @ Mon, 12 Feb 2018 03:40:04: End command message. | |
| 105 INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.tex | |
| 106 INFO @ Mon, 12 Feb 2018 03:40:04: Command message: | |
| 107 INFO @ Mon, 12 Feb 2018 03:40:04: | |
| 108 INFO @ Mon, 12 Feb 2018 03:40:04: End command message. | |
| 109 INFO @ Mon, 12 Feb 2018 03:40:04: Running command: cd ./; rm -rf output_summary.toc | |
| 110 INFO @ Mon, 12 Feb 2018 03:40:04: Command message: | |
| 111 INFO @ Mon, 12 Feb 2018 03:40:04: | |
| 112 INFO @ Mon, 12 Feb 2018 03:40:04: End command message. |