comparison test-data/out.test.log.txt @ 2:82a180e6b582 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
author iuc
date Wed, 04 Apr 2018 11:03:05 -0400
parents d95eae71878e
children
comparison
equal deleted inserted replaced
1:80cf607159ae 2:82a180e6b582
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 1 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
2 INFO @ Mon, 12 Feb 2018 03:40:01: Welcome to MAGeCK v0.5.7. Command: test 2 INFO @ Mon, 26 Mar 2018 08:37:53: 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 3 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
4 INFO @ Mon, 12 Feb 2018 03:40:01: Processing 1 lines.. 4 INFO @ Mon, 26 Mar 2018 08:37:53: Processing 1 lines..
5 DEBUG @ Mon, 12 Feb 2018 03:40:01: Parsing error in line 1 (usually the header line). Skip this line. 5 DEBUG @ Mon, 26 Mar 2018 08:37:53: Parsing error in line 1 (usually the header line). Skip this line.
6 INFO @ Mon, 12 Feb 2018 03:40:01: Loaded 999 records. 6 INFO @ Mon, 26 Mar 2018 08:37:53: 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. 7 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.
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. 8 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.
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. 9 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.
10 DEBUG @ Mon, 12 Feb 2018 03:40:01: Setting up the visualization module... 10 DEBUG @ Mon, 26 Mar 2018 08:37:53: Setting up the visualization module...
11 DEBUG @ Mon, 12 Feb 2018 03:40:01: Given sample labels: HL60.final,KBM7.final 11 DEBUG @ Mon, 26 Mar 2018 08:37:53: Given sample labels: HL60_final,KBM7_final
12 DEBUG @ Mon, 12 Feb 2018 03:40:01: Converted index: 2 3 12 DEBUG @ Mon, 26 Mar 2018 08:37:53: Converted index: 2 3
13 INFO @ Mon, 12 Feb 2018 03:40:01: Treatment samples:HL60.final,KBM7.final 13 INFO @ Mon, 26 Mar 2018 08:37:53: Treatment samples:HL60_final,KBM7_final
14 INFO @ Mon, 12 Feb 2018 03:40:01: Treatment sample index:2,3 14 INFO @ Mon, 26 Mar 2018 08:37:53: Treatment sample index:2,3
15 DEBUG @ Mon, 12 Feb 2018 03:40:01: Given sample labels: HL60.initial,KBM7.initial 15 DEBUG @ Mon, 26 Mar 2018 08:37:53: Given sample labels: HL60_initial,KBM7_initial
16 DEBUG @ Mon, 12 Feb 2018 03:40:01: Converted index: 0 1 16 DEBUG @ Mon, 26 Mar 2018 08:37:53: Converted index: 0 1
17 INFO @ Mon, 12 Feb 2018 03:40:01: Control samples:HL60.initial,KBM7.initial 17 INFO @ Mon, 26 Mar 2018 08:37:53: Control samples:HL60_initial,KBM7_initial
18 INFO @ Mon, 12 Feb 2018 03:40:01: Control sample index:0,1 18 INFO @ Mon, 26 Mar 2018 08:37:53: 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 19 DEBUG @ Mon, 26 Mar 2018 08:37:53: 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 20 DEBUG @ Mon, 26 Mar 2018 08:37:53: 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 21 INFO @ Mon, 26 Mar 2018 08:37:53: 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 22 INFO @ Mon, 26 Mar 2018 08:37:53: Writing normalized read counts to output.normalized.txt
23 DEBUG @ Mon, 12 Feb 2018 03:40:01: Adjusted model: 1.1175084644498339 3.4299551007579927 23 DEBUG @ Mon, 26 Mar 2018 08:37:53: 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 24 INFO @ Mon, 26 Mar 2018 08:37:53: 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 25 INFO @ Mon, 26 Mar 2018 08:37:53: 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 ... 26 INFO @ Mon, 26 Mar 2018 08:37:53: Use qnorm to reversely calculate sgRNA scores ...
27 DEBUG @ Mon, 12 Feb 2018 03:40:01: lower test FDR cutoff: 0.3283283283283283 27 DEBUG @ Mon, 26 Mar 2018 08:37:53: lower test FDR cutoff: 0.3283283283283283
28 DEBUG @ Mon, 12 Feb 2018 03:40:01: higher test FDR cutoff: 0.34534534534534533 28 DEBUG @ Mon, 26 Mar 2018 08:37:53: 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 29 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
30 INFO @ Mon, 12 Feb 2018 03:40:02: Command message: 30 INFO @ Mon, 26 Mar 2018 08:37:53: Command message:
31 INFO @ Mon, 12 Feb 2018 03:40:02: Welcome to RRA v 0.5.7. 31 INFO @ Mon, 26 Mar 2018 08:37:53: Welcome to RRA v 0.5.7.
32 INFO @ Mon, 12 Feb 2018 03:40:02: Skipping gene NA for permutation ... 32 INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene NA for permutation ...
33 INFO @ Mon, 12 Feb 2018 03:40:02: Skipping gene na for permutation ... 33 INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene na for permutation ...
34 INFO @ Mon, 12 Feb 2018 03:40:02: Reading input file... 34 INFO @ Mon, 26 Mar 2018 08:37:53: Reading input file...
35 INFO @ Mon, 12 Feb 2018 03:40:02: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 35 INFO @ Mon, 26 Mar 2018 08:37:53: 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... 36 INFO @ Mon, 26 Mar 2018 08:37:53: Computing lo-values for each group...
37 INFO @ Mon, 12 Feb 2018 03:40:02: Computing false discovery rate... 37 INFO @ Mon, 26 Mar 2018 08:37:53: 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. 38 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.
39 INFO @ Mon, 12 Feb 2018 03:40:02: Permuting genes with 9 sgRNAs... 39 INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 9 sgRNAs...
40 INFO @ Mon, 12 Feb 2018 03:40:02: Permuting genes with 10 sgRNAs... 40 INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 10 sgRNAs...
41 INFO @ Mon, 12 Feb 2018 03:40:02: Number of genes under FDR adjustment: 100 41 INFO @ Mon, 26 Mar 2018 08:37:53: Number of genes under FDR adjustment: 100
42 INFO @ Mon, 12 Feb 2018 03:40:02: Saving to output file... 42 INFO @ Mon, 26 Mar 2018 08:37:53: Saving to output file...
43 INFO @ Mon, 12 Feb 2018 03:40:02: RRA completed. 43 INFO @ Mon, 26 Mar 2018 08:37:53: RRA completed.
44 INFO @ Mon, 12 Feb 2018 03:40:02: 44 INFO @ Mon, 26 Mar 2018 08:37:53:
45 INFO @ Mon, 12 Feb 2018 03:40:02: End command message. 45 INFO @ Mon, 26 Mar 2018 08:37:53: 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 46 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
47 INFO @ Mon, 12 Feb 2018 03:40:03: Command message: 47 INFO @ Mon, 26 Mar 2018 08:37:53: Command message:
48 INFO @ Mon, 12 Feb 2018 03:40:03: Welcome to RRA v 0.5.7. 48 INFO @ Mon, 26 Mar 2018 08:37:53: Welcome to RRA v 0.5.7.
49 INFO @ Mon, 12 Feb 2018 03:40:03: Skipping gene NA for permutation ... 49 INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene NA for permutation ...
50 INFO @ Mon, 12 Feb 2018 03:40:03: Skipping gene na for permutation ... 50 INFO @ Mon, 26 Mar 2018 08:37:53: Skipping gene na for permutation ...
51 INFO @ Mon, 12 Feb 2018 03:40:03: Reading input file... 51 INFO @ Mon, 26 Mar 2018 08:37:53: Reading input file...
52 INFO @ Mon, 12 Feb 2018 03:40:03: Summary: 999 sgRNAs, 100 genes, 1 lists; skipped sgRNAs:0 52 INFO @ Mon, 26 Mar 2018 08:37:53: 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... 53 INFO @ Mon, 26 Mar 2018 08:37:53: Computing lo-values for each group...
54 INFO @ Mon, 12 Feb 2018 03:40:03: Computing false discovery rate... 54 INFO @ Mon, 26 Mar 2018 08:37:53: 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. 55 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.
56 INFO @ Mon, 12 Feb 2018 03:40:03: Permuting genes with 9 sgRNAs... 56 INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 9 sgRNAs...
57 INFO @ Mon, 12 Feb 2018 03:40:03: Permuting genes with 10 sgRNAs... 57 INFO @ Mon, 26 Mar 2018 08:37:53: Permuting genes with 10 sgRNAs...
58 INFO @ Mon, 12 Feb 2018 03:40:03: Number of genes under FDR adjustment: 100 58 INFO @ Mon, 26 Mar 2018 08:37:53: Number of genes under FDR adjustment: 100
59 INFO @ Mon, 12 Feb 2018 03:40:03: Saving to output file... 59 INFO @ Mon, 26 Mar 2018 08:37:53: Saving to output file...
60 INFO @ Mon, 12 Feb 2018 03:40:03: RRA completed. 60 INFO @ Mon, 26 Mar 2018 08:37:53: RRA completed.
61 INFO @ Mon, 12 Feb 2018 03:40:03: 61 INFO @ Mon, 26 Mar 2018 08:37:53:
62 INFO @ Mon, 12 Feb 2018 03:40:03: End command message. 62 INFO @ Mon, 26 Mar 2018 08:37:53: End command message.
63 DEBUG @ Mon, 12 Feb 2018 03:40:03: Sorting the merged items by negative selection... 63 DEBUG @ Mon, 26 Mar 2018 08:37:53: 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 64 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
65 DEBUG @ Mon, 12 Feb 2018 03:40:03: Column index:3 65 DEBUG @ Mon, 26 Mar 2018 08:37:53: 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 66 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
67 DEBUG @ Mon, 12 Feb 2018 03:40:03: Column index:9 67 DEBUG @ Mon, 26 Mar 2018 08:37:53: Column index:9
68 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.plow.txt 68 INFO @ Mon, 26 Mar 2018 08:37:53: Running command: rm output.plow.txt
69 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.phigh.txt 69 INFO @ Mon, 26 Mar 2018 08:37:53: Running command: rm output.phigh.txt
70 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.gene.low.txt 70 INFO @ Mon, 26 Mar 2018 08:37:54: Running command: rm output.gene.low.txt
71 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: rm output.gene.high.txt 71 INFO @ Mon, 26 Mar 2018 08:37:54: Running command: rm output.gene.high.txt
72 INFO @ Mon, 12 Feb 2018 03:40:03: Running command: cd ./; Rscript output.R 72 INFO @ Mon, 26 Mar 2018 08:37:54: Running command: cd ./; Rscript output.R
73 INFO @ Mon, 12 Feb 2018 03:40:04: Command message: 73 INFO @ Mon, 26 Mar 2018 08:37:59: Command message:
74 INFO @ Mon, 12 Feb 2018 03:40:04: null device 74 INFO @ Mon, 26 Mar 2018 08:37:59: null device
75 INFO @ Mon, 12 Feb 2018 03:40:04: 1 75 INFO @ Mon, 26 Mar 2018 08:37:59: 1
76 INFO @ Mon, 12 Feb 2018 03:40:04: Writing to file output_summary.tex 76 INFO @ Mon, 26 Mar 2018 08:37:59: Writing to file output_summary.tex
77 INFO @ Mon, 12 Feb 2018 03:40:04: Processing code chunks with options ... 77 INFO @ Mon, 26 Mar 2018 08:37:59: 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) 78 INFO @ Mon, 26 Mar 2018 08:37:59: 1 : keep.source term verbatim (label = funcdef, output_summary.Rnw:27)
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90 INFO @ Mon, 12 Feb 2018 03:40:04: 90 INFO @ Mon, 26 Mar 2018 08:37:59:
91 INFO @ Mon, 12 Feb 2018 03:40:04: You can now run (pdf)latex on ‘output_summary.tex’ 91 INFO @ Mon, 26 Mar 2018 08:37:59: 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) : 92 INFO @ Mon, 26 Mar 2018 08:37:59:
93 INFO @ Mon, 12 Feb 2018 03:40:04: pdflatex is not available 93 INFO @ Mon, 26 Mar 2018 08:37:59: End command message.
94 INFO @ Mon, 12 Feb 2018 03:40:04: Execution halted 94 INFO @ Mon, 26 Mar 2018 08:37:59: Running command: cd ./; rm -rf output_summary-*.pdf
95 INFO @ Mon, 12 Feb 2018 03:40:04: 95 INFO @ Mon, 26 Mar 2018 08:37:59: Command message:
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