# HG changeset patch # User devteam # Date 1638548877 0 # Node ID 1a6979fbd544bc5e8043abb15fb145bb5c1277c0 # Parent 201d8e7dfc43b3e4125ebbe41688c259ecc79a50 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat commit 1370bb21ee5712a13a26d289065406c5d489b8cc" diff -r 201d8e7dfc43 -r 1a6979fbd544 ccat_wrapper.py --- a/ccat_wrapper.py Tue Jul 21 14:13:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -import sys, subprocess, tempfile, shutil, os.path - -CCAT_BINARY = "CCAT" - -def get_top_count( filename ): - for line in open( filename ): - if line.startswith( 'outputNum' ): - return int( line.split()[-1].strip() ) - -def stop_err( tmp_dir, exception ): - print >> sys.stderr, "Error running CCAT." - shutil.rmtree( tmp_dir ) #some error has occurred, provide info and remove possibly non-empty temp directory - raise exception - -def main(): - input_tag_file = sys.argv[1] - input_control_file = sys.argv[2] - chrom_info_file = sys.argv[3] - input_config_file = sys.argv[4] - project_name = sys.argv[5] - output_peak_file = sys.argv[6] - output_region_file = sys.argv[7] - output_top_file = sys.argv[8] - output_log_file = sys.argv[9] - - tmp_dir = tempfile.mkdtemp() - try: - assert os.path.exists( chrom_info_file ), "The required chromosome length file does not exist." - proc = subprocess.Popen( args="%s %s > %s" % ( CCAT_BINARY, " ".join( map( lambda x: "'%s'" % x, [ input_tag_file, input_control_file, chrom_info_file, input_config_file, project_name ] ) ), output_log_file ), shell=True, cwd=tmp_dir ) - proc.wait() - if proc.returncode: - raise Exception( "Error code: %i" % proc.returncode ) - output_num = get_top_count( input_config_file ) - shutil.move( os.path.join( tmp_dir, "%s.significant.peak" % project_name ), output_peak_file ) - shutil.move( os.path.join( tmp_dir, "%s.significant.region" % project_name ), output_region_file ) - shutil.move( os.path.join( tmp_dir, "%s.top%i.peak" % ( project_name, output_num ) ), output_top_file ) - except Exception, e: - return stop_err( tmp_dir, e ) - os.rmdir( tmp_dir ) #clean up empty temp working directory - -if __name__ == "__main__": main() diff -r 201d8e7dfc43 -r 1a6979fbd544 ccat_wrapper.xml --- a/ccat_wrapper.xml Tue Jul 21 14:13:34 2015 -0400 +++ b/ccat_wrapper.xml Fri Dec 03 16:27:57 2021 +0000 @@ -1,23 +1,49 @@ - + Control-based ChIP-seq Analysis Tool - CCAT + ccat - ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' - #if str( $options_type[ 'options_type_selector' ] ) == 'advanced': - '$input_advanced_config_file' - #else: - '${ options_type.input_config_file.fields.path }' - #end if - 'CCAT in Galaxy' - '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file' + + + + + + + + - - - - - - + + @@ -45,23 +71,24 @@ + - + - + - + @@ -70,78 +97,44 @@ - - #if str( $options_type['options_type_selector' ] ) == 'advanced': -fragmentSize ${options_type[ 'fragment_size' ]} -slidingWinSize ${options_type[ 'sliding_window_size' ]} -movingStep ${options_type[ 'moving_step' ]} -isStrandSensitiveMode ${options_type[ 'is_strand_sensitive_mode' ]} -minCount ${options_type[ 'min_count' ]} -outputNum ${options_type[ 'output_num' ]} -randomSeed ${options_type[ 'random_seed' ]} -minScore ${options_type[ 'min_score' ]} -bootstrapPass ${options_type[ 'bootstrap_pass' ]} -#end if - - - + + - - - - + + + + - - - - + + + + + - - + + - - - - - + + + + + + - - **What it does** This tool allows ChIP-seq peak/region calling using CCAT. -View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm. - ------- - -**Citation** - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - +View the original CCAT documentation: https://www.comp.nus.edu.sg/~bioinfo/CCAT3.0/ 10.1093/bioinformatics/btq128 diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/1.interval --- a/test-data/1.interval Tue Jul 21 14:13:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -chr1 4348187 4348589 3.70 4.90 2.55 0.24 0.46 -chr1 4488177 4488442 4.03 5.77 1.92 -0.67 0.81 -chr1 4774091 4774440 8.07 8.33 7.82 0.85 -0.40 -chr1 4800122 4800409 6.40 7.35 5.44 1.19 -0.42 -chr1 4878925 4879277 2.18 0.28 4.93 -0.96 1.24 diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/1.txt --- a/test-data/1.txt Tue Jul 21 14:13:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -chr1 4225 19670 -chr10 6 8 -chr1 24417 24420 -chr6_hla_hap2 0 150 -chr2 1 5 -chr10 2 10 -chr1 30 55 -chrY 1 20 -chr1 1225979 42287290 -chr10 7 8 diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/2.interval --- a/test-data/2.interval Tue Jul 21 14:13:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -chrX 151117436 151117437 + 0.14351 -chrX 151117437 151117438 + 0.139843 -chrX 151117438 151117439 + 0.132509 -chrX 151117439 151117440 + 0.139843 -chrX 151117440 151117441 + 0.169179 -chrX 151117441 151117442 + 0.257185 -chrX 151117442 151117443 + 0.319523 -chrX 151117443 151117444 + 0.367193 -chrX 151117444 151117445 + 0.400195 -chrX 151117445 151117446 + 0.425864 -chrX 151117446 151117447 + 0.444198 -chrX 151117447 151117448 + 0.455199 -chrX 151117448 151117449 + 0.462533 -chrX 151117449 151117450 + 0.4662 diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/2.txt --- a/test-data/2.txt Tue Jul 21 14:13:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -chr1 4225 19670 -chr10 6 8 -chr1 24417 24420 -chr6_hla_hap2 0 150 -chr2 1 5 -chr1 30 55 -chrY 1 20 -chr1 1225979 42287290 diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/ES_CTCF_chr19.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ES_CTCF_chr19.bed Fri Dec 03 16:27:57 2021 +0000 @@ -0,0 +1,103146 @@ +chr19 35798438 35798462 0 0 - 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+chr19 6416987 6417011 0 0 - +chr19 37667796 37667820 0 0 - +chr19 59009963 59009987 0 0 - +chr19 15734906 15734930 0 0 + +chr19 46087296 46087320 0 0 - +chr19 43532425 43532449 0 0 - +chr19 35685220 35685244 0 0 - +chr19 11043590 11043614 0 0 + +chr19 47557116 47557140 0 0 - +chr19 27462279 27462303 0 0 - +chr19 57450818 57450842 0 0 + diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/ES_CTCF_chr19.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ES_CTCF_chr19.log Fri Dec 03 16:27:57 2021 +0000 @@ -0,0 +1,53 @@ +chromosome length information read. chromNum = 1! +config file read. +fragmentSize = 200 +isStrandSensitiveMode = 1 +slidingWinSize = 300 +movingStep = 10 +outputNum = 100000 +minCount = 3 +minScore = 5.000000 +bootstrapPass = 50 +randSeed = 123456 +reading tag files...... +103146 tags in L1, 97149 tags in L2. +tag file read. +pre-processing...... +pre-processing finished. +estimating noise rate...... +iteration 0: nr=0.669578 +iteration 1: nr=0.613605 +iteration 2: nr=0.593059 +iteration 3: nr=0.586303 +iteration 4: nr=0.583061 +iteration 5: nr=0.583061 +iteration 6: nr=0.582451 +iteration 7: nr=0.586573 +iteration 8: nr=0.583271 +iteration 9: nr=0.581424 +iteration 10: nr=0.585253 +iteration 11: nr=0.583917 +iteration 12: nr=0.583446 +iteration 13: nr=0.581896 +iteration 14: nr=0.583084 +iteration 15: nr=0.581582 +iteration 16: nr=0.582966 +iteration 17: nr=0.583596 +iteration 18: nr=0.586691 +iteration 19: nr=0.584954 +noise rate = 0.583743 +peak-finding...... +chr19......2946 candidate peaks. +peak-finding finished. +Significance Analysis...... +estimating paramters...... +smoothing factor = 20.048787 +estimating local FDR..... +FDR at the threshold 5.000000 is 0.999000. You may want to adjust the threshold by inspecting the output files. +post-processing...... +chr19......finished. +post-processing finished. +Significance analysis finished. +saving results....... +results saved. +CCAT process completed! diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/ES_CTCF_chr19.significant.peak --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ES_CTCF_chr19.significant.peak Fri Dec 03 16:27:57 2021 +0000 @@ -0,0 +1,2946 @@ +chr19 44636155 44635690 44637010 138 2 281.402772 0.001000 +chr19 44416985 44416460 44417390 101 1 211.604907 0.001000 +chr19 59292915 59292150 59293510 85 1 177.560301 0.001000 +chr19 47936055 47935520 47936450 74 0 159.742535 0.001000 +chr19 40399185 40398760 40399610 74 0 159.742535 0.001000 +chr19 8645395 8645010 8646090 73 0 157.583853 0.001000 +chr19 24368185 24367620 24369230 75 1 157.286191 0.001000 +chr19 6305005 6304590 6305500 72 0 155.425170 0.001000 +chr19 45297825 45297050 45298220 70 0 151.107804 0.001000 +chr19 41125035 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test-data/ES_CTCF_chr19.top100000.peak --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ES_CTCF_chr19.top100000.peak Fri Dec 03 16:27:57 2021 +0000 @@ -0,0 +1,2946 @@ +chr19 44636155 44635690 44637010 138 2 281.402772 0.001000 +chr19 44416985 44416460 44417390 101 1 211.604907 0.001000 +chr19 59292915 59292150 59293510 85 1 177.560301 0.001000 +chr19 47936055 47935520 47936450 74 0 159.742535 0.001000 +chr19 40399185 40398760 40399610 74 0 159.742535 0.001000 +chr19 8645395 8645010 8646090 73 0 157.583853 0.001000 +chr19 24368185 24367620 24369230 75 1 157.286191 0.001000 +chr19 6305005 6304590 6305500 72 0 155.425170 0.001000 +chr19 45297825 45297050 45298220 70 0 151.107804 0.001000 +chr19 41125035 41124470 41125450 68 0 146.790438 0.001000 +chr19 40444995 40444590 40445440 67 0 144.631755 0.001000 +chr19 44349275 44347770 44349670 67 0 144.631755 0.001000 +chr19 41496115 41495440 41496530 67 0 144.631755 0.001000 +chr19 10569835 10569400 10570520 66 0 142.473072 0.001000 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rs1009806 19373138 G ADD 1021 -1.334 -3.756 0.0001826 -1 rs1009806 19373138 G GENO_2DF 1021 NA 19.36 6.244e-05 -1 rs873654 29550948 A DOMDEV 1012 1.526 3.6 0.0003339 -1 rs10489527 36800027 C ADD 1016 12.67 4.114 4.211e-05 -1 rs10489527 36800027 C DOMDEV 1016 -13.05 -4.02 6.249e-05 diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/ccat_configurations.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ccat_configurations.loc Fri Dec 03 16:27:57 2021 +0000 @@ -0,0 +1,1 @@ +config_TF config_TF ${__HERE__}/config_TF.txt diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/chipseq_enriched.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chipseq_enriched.bed Fri Dec 03 16:27:57 2021 +0000 @@ -0,0 +1,10000 @@ +chr1 3002169 3002205 region_0 0 - +chr1 3002286 3002322 region_1 0 + +chr1 3002418 3002454 region_2 0 - +chr1 3002729 3002765 region_3 0 + +chr1 3002805 3002841 region_4 0 + +chr1 3002805 3002841 region_5 0 + +chr1 3003028 3003064 region_6 0 + +chr1 3003127 3003163 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region_9904 0 + +chr1 4647696 4647732 region_9905 0 - +chr1 4647722 4647758 region_9906 0 + +chr1 4647755 4647791 region_9907 0 + +chr1 4648124 4648160 region_9908 0 - +chr1 4648129 4648165 region_9909 0 - +chr1 4648179 4648215 region_9910 0 - +chr1 4648461 4648497 region_9911 0 + +chr1 4648523 4648559 region_9912 0 - +chr1 4648532 4648568 region_9913 0 + +chr1 4648554 4648590 region_9914 0 - +chr1 4650071 4650107 region_9915 0 + +chr1 4650119 4650155 region_9916 0 - +chr1 4650645 4650681 region_9917 0 - +chr1 4652025 4652061 region_9918 0 - +chr1 4652316 4652352 region_9919 0 + +chr1 4652334 4652370 region_9920 0 + +chr1 4652368 4652404 region_9921 0 - +chr1 4652487 4652523 region_9922 0 - +chr1 4652666 4652702 region_9923 0 + +chr1 4652701 4652737 region_9924 0 - +chr1 4653073 4653109 region_9925 0 - +chr1 4653175 4653211 region_9926 0 - +chr1 4653188 4653224 region_9927 0 + +chr1 4653199 4653235 region_9928 0 - +chr1 4653277 4653313 region_9929 0 + +chr1 4653345 4653381 region_9930 0 + +chr1 4653387 4653423 region_9931 0 - +chr1 4653471 4653507 region_9932 0 - +chr1 4653503 4653539 region_9933 0 - +chr1 4653574 4653610 region_9934 0 - +chr1 4653665 4653701 region_9935 0 + +chr1 4655248 4655284 region_9936 0 + +chr1 4655485 4655521 region_9937 0 + +chr1 4656708 4656744 region_9938 0 - +chr1 4656721 4656757 region_9939 0 - +chr1 4656752 4656788 region_9940 0 + +chr1 4656810 4656846 region_9941 0 - +chr1 4657008 4657044 region_9942 0 - +chr1 4657224 4657260 region_9943 0 - +chr1 4657264 4657300 region_9944 0 + +chr1 4657354 4657390 region_9945 0 + +chr1 4657366 4657402 region_9946 0 + +chr1 4657389 4657425 region_9947 0 + +chr1 4657454 4657490 region_9948 0 + +chr1 4657590 4657626 region_9949 0 - +chr1 4657717 4657753 region_9950 0 - +chr1 4657724 4657760 region_9951 0 - +chr1 4657774 4657810 region_9952 0 + +chr1 4657836 4657872 region_9953 0 - +chr1 4657909 4657945 region_9954 0 - +chr1 4657912 4657948 region_9955 0 + +chr1 4657928 4657964 region_9956 0 - +chr1 4657951 4657987 region_9957 0 + +chr1 4658311 4658347 region_9958 0 - +chr1 4658321 4658357 region_9959 0 + +chr1 4658371 4658407 region_9960 0 + +chr1 4658397 4658433 region_9961 0 + +chr1 4658487 4658523 region_9962 0 + +chr1 4658664 4658700 region_9963 0 - +chr1 4658713 4658749 region_9964 0 - +chr1 4658824 4658860 region_9965 0 - +chr1 4658866 4658902 region_9966 0 - +chr1 4658905 4658941 region_9967 0 + +chr1 4658955 4658991 region_9968 0 + +chr1 4658971 4659007 region_9969 0 - +chr1 4659035 4659071 region_9970 0 - +chr1 4659244 4659280 region_9971 0 - +chr1 4659387 4659423 region_9972 0 + +chr1 4659465 4659501 region_9973 0 - +chr1 4659470 4659506 region_9974 0 - +chr1 4659504 4659540 region_9975 0 - +chr1 4659504 4659540 region_9976 0 - +chr1 4659511 4659547 region_9977 0 - +chr1 4659523 4659559 region_9978 0 + +chr1 4659530 4659566 region_9979 0 - +chr1 4659563 4659599 region_9980 0 - +chr1 4659578 4659614 region_9981 0 - +chr1 4659619 4659655 region_9982 0 + +chr1 4659698 4659734 region_9983 0 + +chr1 4659803 4659839 region_9984 0 + +chr1 4659846 4659882 region_9985 0 + +chr1 4659880 4659916 region_9986 0 - +chr1 4660125 4660161 region_9987 0 - +chr1 4660236 4660272 region_9988 0 + +chr1 4660334 4660370 region_9989 0 + +chr1 4660404 4660440 region_9990 0 + +chr1 4660431 4660467 region_9991 0 - +chr1 4661109 4661145 region_9992 0 + +chr1 4661186 4661222 region_9993 0 + +chr1 4661332 4661368 region_9994 0 + +chr1 4661506 4661542 region_9995 0 + +chr1 4661557 4661593 region_9996 0 - +chr1 4661619 4661655 region_9997 0 - +chr1 4662104 4662140 region_9998 0 - +chr1 4662148 4662184 region_9999 0 + diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/chipseq_input.bed.gz Binary file test-data/chipseq_input.bed.gz has changed diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/config_TF.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/config_TF.txt Fri Dec 03 16:27:57 2021 +0000 @@ -0,0 +1,9 @@ +fragmentSize 200 +slidingWinSize 300 +movingStep 10 +isStrandSensitiveMode 1 +minCount 3 +outputNum 100000 +randomSeed 123456 +minScore 5.0 +bootstrapPass 50 diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/genome_length_mm8_chr19.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_length_mm8_chr19.txt Fri Dec 03 16:27:57 2021 +0000 @@ -0,0 +1,1 @@ +chr19 61321190 \ No newline at end of file diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/hg18.len --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg18.len Fri Dec 03 16:27:57 2021 +0000 @@ -0,0 +1,49 @@ +1 chr1 247249719 +2 chr2 242951149 +3 chr3 199501827 +4 chr4 191273063 +5 chr5 180857866 +6 chr6 170899992 +7 chr7 158821424 +8 chr8 146274826 +9 chr9 140273252 +10 chr10 135374737 +11 chr11 134452384 +12 chr12 132349534 +13 chr13 114142980 +14 chr14 106368585 +15 chr15 100338915 +16 chr16 88827254 +17 chr17 78774742 +18 chr18 76117153 +19 chr19 63811651 +20 chr20 62435964 +21 chr21 46944323 +22 chr22 49691432 +23 chrX 154913754 +24 chrY 57772954 + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/peakcalling_ccat/3.0/ccat_test_log_out_1.txt --- a/test-data/peakcalling_ccat/3.0/ccat_test_log_out_1.txt Tue Jul 21 14:13:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,131 +0,0 @@ -chromosome length information read. chromNum = 49! -config file read. -fragmentSize = 200 -isStrandSensitiveMode = 0 -slidingWinSize = 500 -movingStep = 50 -outputNum = 100000 -minCount = 4 -minScore = 5.000000 -bootstrapPass = 50 -randSeed = 123456 -reading tag files...... -10000 tags in L1, 10000 tags in L2. -tag file read. -pre-processing...... -pre-processing finished. -estimating noise rate...... -not enough reads for noise rate estimation. -noise rate estimation failed. noise rate set to be 1.0 -noise rate = 1.000000 -peak-finding...... -chr1......884 candidate peaks. -chr1_random......0 candidate peaks. -chr10......0 candidate peaks. -chr10_random......0 candidate peaks. -chr11......0 candidate peaks. -chr11_random......0 candidate peaks. -chr12......0 candidate peaks. -chr13......0 candidate peaks. -chr13_random......0 candidate peaks. -chr14......0 candidate peaks. -chr15......0 candidate peaks. -chr15_random......0 candidate peaks. -chr16......0 candidate peaks. -chr16_random......0 candidate peaks. -chr17......0 candidate peaks. -chr17_random......0 candidate peaks. -chr18......0 candidate peaks. -chr18_random......0 candidate peaks. -chr19......0 candidate peaks. -chr19_random......0 candidate peaks. -chr2......0 candidate peaks. -chr2_random......0 candidate peaks. -chr20......0 candidate peaks. -chr21......0 candidate peaks. -chr21_random......0 candidate peaks. -chr22......0 candidate peaks. -chr22_random......0 candidate peaks. -chr22_h2_hap1......0 candidate peaks. -chr3......0 candidate peaks. -chr3_random......0 candidate peaks. -chr4......0 candidate peaks. -chr4_random......0 candidate peaks. -chr5......0 candidate peaks. -chr5_random......0 candidate peaks. -chr5_h2_hap1......0 candidate peaks. -chr6......0 candidate peaks. -chr6_random......0 candidate peaks. -chr6_cox_hap1......0 candidate peaks. -chr6_qbl_hap2......0 candidate peaks. -chr7......0 candidate peaks. -chr7_random......0 candidate peaks. -chr8......0 candidate peaks. -chr8_random......0 candidate peaks. -chr9......0 candidate peaks. -chr9_random......0 candidate peaks. -chrM......0 candidate peaks. -chrX......0 candidate peaks. -chrX_random......0 candidate peaks. -chrY......0 candidate peaks. -peak-finding finished. -Significance Analysis...... -estimating paramters...... -smoothing factor = 0.356298 -estimating local FDR..... -FDR at the threshold 5.000000 is 0.999000. You may want to adjust the threshold by inspecting the output files. -post-processing...... -chr1......finished. -chr1_random......finished. -chr10......finished. -chr10_random......finished. -chr11......finished. -chr11_random......finished. -chr12......finished. -chr13......finished. -chr13_random......finished. -chr14......finished. -chr15......finished. -chr15_random......finished. -chr16......finished. -chr16_random......finished. -chr17......finished. -chr17_random......finished. -chr18......finished. -chr18_random......finished. -chr19......finished. -chr19_random......finished. -chr2......finished. -chr2_random......finished. -chr20......finished. -chr21......finished. -chr21_random......finished. -chr22......finished. -chr22_random......finished. -chr22_h2_hap1......finished. -chr3......finished. -chr3_random......finished. -chr4......finished. -chr4_random......finished. -chr5......finished. -chr5_random......finished. -chr5_h2_hap1......finished. -chr6......finished. -chr6_random......finished. -chr6_cox_hap1......finished. -chr6_qbl_hap2......finished. -chr7......finished. -chr7_random......finished. -chr8......finished. -chr8_random......finished. -chr9......finished. -chr9_random......finished. -chrM......finished. -chrX......finished. -chrX_random......finished. -chrY......finished. -post-processing finished. -Significance analysis finished. -saving results....... -results saved. -CCAT process completed! diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/peakcalling_ccat/3.0/ccat_test_log_out_2.txt --- a/test-data/peakcalling_ccat/3.0/ccat_test_log_out_2.txt Tue Jul 21 14:13:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,131 +0,0 @@ -chromosome length information read. chromNum = 49! -config file read. -fragmentSize = 200 -isStrandSensitiveMode = 0 -slidingWinSize = 1000 -movingStep = 50 -outputNum = 100000 -minCount = 4 -minScore = 5.000000 -bootstrapPass = 50 -randSeed = 123456 -reading tag files...... -10000 tags in L1, 10000 tags in L2. -tag file read. -pre-processing...... -pre-processing finished. -estimating noise rate...... -not enough reads for noise rate estimation. -noise rate estimation failed. noise rate set to be 1.0 -noise rate = 1.000000 -peak-finding...... -chr1......673 candidate peaks. -chr1_random......0 candidate peaks. -chr10......0 candidate peaks. -chr10_random......0 candidate peaks. -chr11......0 candidate peaks. -chr11_random......0 candidate peaks. -chr12......0 candidate peaks. -chr13......0 candidate peaks. -chr13_random......0 candidate peaks. -chr14......0 candidate peaks. -chr15......0 candidate peaks. -chr15_random......0 candidate peaks. -chr16......0 candidate peaks. -chr16_random......0 candidate peaks. -chr17......0 candidate peaks. -chr17_random......0 candidate peaks. -chr18......0 candidate peaks. -chr18_random......0 candidate peaks. -chr19......0 candidate peaks. -chr19_random......0 candidate peaks. -chr2......0 candidate peaks. -chr2_random......0 candidate peaks. -chr20......0 candidate peaks. -chr21......0 candidate peaks. -chr21_random......0 candidate peaks. -chr22......0 candidate peaks. -chr22_random......0 candidate peaks. -chr22_h2_hap1......0 candidate peaks. -chr3......0 candidate peaks. -chr3_random......0 candidate peaks. -chr4......0 candidate peaks. -chr4_random......0 candidate peaks. -chr5......0 candidate peaks. -chr5_random......0 candidate peaks. -chr5_h2_hap1......0 candidate peaks. -chr6......0 candidate peaks. -chr6_random......0 candidate peaks. -chr6_cox_hap1......0 candidate peaks. -chr6_qbl_hap2......0 candidate peaks. -chr7......0 candidate peaks. -chr7_random......0 candidate peaks. -chr8......0 candidate peaks. -chr8_random......0 candidate peaks. -chr9......0 candidate peaks. -chr9_random......0 candidate peaks. -chrM......0 candidate peaks. -chrX......0 candidate peaks. -chrX_random......0 candidate peaks. -chrY......0 candidate peaks. -peak-finding finished. -Significance Analysis...... -estimating paramters...... -smoothing factor = 0.287387 -estimating local FDR..... -FDR at the threshold 5.000000 is 0.999000. You may want to adjust the threshold by inspecting the output files. -post-processing...... -chr1......finished. -chr1_random......finished. -chr10......finished. -chr10_random......finished. -chr11......finished. -chr11_random......finished. -chr12......finished. -chr13......finished. -chr13_random......finished. -chr14......finished. -chr15......finished. -chr15_random......finished. -chr16......finished. -chr16_random......finished. -chr17......finished. -chr17_random......finished. -chr18......finished. -chr18_random......finished. -chr19......finished. -chr19_random......finished. -chr2......finished. -chr2_random......finished. -chr20......finished. -chr21......finished. -chr21_random......finished. -chr22......finished. -chr22_random......finished. -chr22_h2_hap1......finished. -chr3......finished. -chr3_random......finished. -chr4......finished. -chr4_random......finished. -chr5......finished. -chr5_random......finished. -chr5_h2_hap1......finished. -chr6......finished. -chr6_random......finished. -chr6_cox_hap1......finished. -chr6_qbl_hap2......finished. -chr7......finished. -chr7_random......finished. -chr8......finished. -chr8_random......finished. -chr9......finished. -chr9_random......finished. -chrM......finished. -chrX......finished. -chrX_random......finished. -chrY......finished. -post-processing finished. -Significance analysis finished. -saving results....... -results saved. -CCAT process completed! diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match --- a/test-data/peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match Tue Jul 21 14:13:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,382 +0,0 @@ -chr1 4760025 4756750 4762650 128 0 399\.\d+ 0\.133000 -chr1 4761475 4756750 4762650 74 0 230\.\d+ 0\.133000 -chr1 4771725 4768050 4778800 37 0 115\.\d+ 0\.133000 -chr1 5061925 5060800 5063500 15 0 46\.\d+ 0\.133000 -chr1 5174925 5172300 5175650 15 0 46\.\d+ 0\.133000 -chr1 5198225 5193500 5203550 13 0 40\.\d+ 0\.133000 -chr1 5094525 5090900 5098600 12 0 37\.\d+ 0\.133000 -chr1 5649775 5646050 5655200 12 0 37\.\d+ 0\.133000 -chr1 4764325 4763100 4767650 11 0 34\.\d+ 0\.189000 -chr1 5250175 5247500 5252250 11 0 34\.\d+ 0\.189000 -chr1 4861125 4856150 4863100 11 0 34\.\d+ 0\.189000 -chr1 5202075 5193500 5203550 11 0 34\.\d+ 0\.189000 -chr1 4961625 4952100 4964300 11 0 34\.\d+ 0\.189000 -chr1 4830175 4828350 4831300 11 0 34\.\d+ 0\.189000 -chr1 5177075 5175750 5180950 11 0 34\.\d+ 0\.189000 -chr1 4849575 4842300 4852000 10 0 31\.\d+ 0\.189000 -chr1 4792275 4789000 4793650 10 0 31\.\d+ 0\.189000 -chr1 4996125 4991700 4999350 10 0 31\.\d+ 0\.189000 -chr1 5132325 5128000 5136550 10 0 31\.\d+ 0\.189000 -chr1 5270525 5269800 5276000 10 0 31\.\d+ 0\.189000 -chr1 4716525 4708050 4718500 10 0 31\.\d+ 0\.189000 -chr1 4766575 4763100 4767650 10 0 31\.\d+ 0\.189000 -chr1 4740375 4733200 4746750 10 0 31\.\d+ 0\.189000 -chr1 5594075 5591050 5602000 10 0 31\.\d+ 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-chr1 3559825 3559550 3560150 7 1 5\.\d+ 1\.000000 -chr1 4247375 4247100 4247650 11 2 5\.\d+ 1\.000000 diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match --- a/test-data/peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match Tue Jul 21 14:13:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -chr1 4760225 4725450 4779800 139 0 507\.\d+ 0\.025000 -chr1 5061725 5053400 5068550 19 0 69\.\d+ 0\.025000 -chr1 5094825 5080750 5101500 19 0 69\.\d+ 0\.025000 -chr1 5174775 5163300 5181450 19 0 69\.\d+ 0\.025000 -chr1 5198075 5193000 5227900 17 0 62\.\d+ 0\.025000 -chr1 5593825 5575300 5618600 17 0 62\.\d+ 0\.025000 -chr1 4716275 4707550 4722700 16 0 58\.\d+ 0\.025000 -chr1 4961575 4951600 4964800 15 0 54\.\d+ 0\.025000 -chr1 4996075 4990250 5026600 15 0 54\.\d+ 0\.025000 -chr1 4792775 4788500 4798400 14 0 51\.\d+ 0\.025000 -chr1 4820975 4818750 4863650 14 0 51\.\d+ 0\.025000 -chr1 4892125 4888750 4938450 14 0 51\.\d+ 0\.025000 -chr1 4811575 4798500 4818650 14 0 51\.\d+ 0\.025000 -chr1 5132075 5121600 5140300 14 0 51\.\d+ 0\.025000 -chr1 5078525 5073200 5080700 13 0 47\.\d+ 0\.025000 -chr1 5249925 5247000 5258700 13 0 47\.\d+ 0\.025000 -chr1 4666375 4662050 4671350 13 0 47\.\d+ 0\.025000 -chr1 5649475 5645550 5668850 13 0 47\.\d+ 0\.025000 -chr1 4872625 4871150 4888250 12 0 43\.\d+ 0\.025000 -chr1 5510825 5501200 5517200 12 0 43\.\d+ 0\.025000 -chr1 4967025 4965050 4970850 12 0 43\.\d+ 0\.025000 -chr1 5306825 5300700 5319250 12 0 43\.\d+ 0\.025000 -chr1 5270275 5269300 5281550 11 0 40\.\d+ 0\.034000 -chr1 5570325 5567450 5573850 11 0 40\.\d+ 0\.034000 -chr1 5106525 5105050 5117450 11 0 40\.\d+ 0\.034000 -chr1 5045675 5044200 5048700 11 0 40\.\d+ 0\.034000 -chr1 5532875 5521900 5536850 11 0 40\.\d+ 0\.034000 -chr1 5429475 5427200 5435250 11 0 40\.\d+ 0\.034000 -chr1 5726025 5720500 5731000 11 0 40\.\d+ 0\.034000 -chr1 5386675 5368500 5389350 11 0 40\.\d+ 0\.034000 -chr1 4692075 4673000 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5693900 5701400 7 0 25\.\d+ 0\.135000 -chr1 5699925 5693900 5701400 4 0 14\.\d+ 1\.000000 -chr1 5706725 5703650 5710750 8 0 29\.\d+ 0\.034000 -chr1 5712725 5711700 5719950 4 0 14\.\d+ 1\.000000 -chr1 5716025 5711700 5719950 7 0 25\.\d+ 0\.135000 -chr1 5718625 5711700 5719950 7 0 25\.\d+ 0\.135000 -chr1 5722875 5720500 5731000 5 0 18\.\d+ 0\.199000 -chr1 5726025 5720500 5731000 11 0 40\.\d+ 0\.034000 -chr1 5742375 5741000 5748200 7 0 25\.\d+ 0\.135000 -chr1 5744425 5741000 5748200 6 0 21\.\d+ 0\.135000 -chr1 5746175 5741000 5748200 9 0 32\.\d+ 0\.034000 -chr1 5751925 5749150 5753500 7 0 25\.\d+ 0\.135000 diff -r 201d8e7dfc43 -r 1a6979fbd544 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Dec 03 16:27:57 2021 +0000 @@ -0,0 +1,8 @@ + + + + + value, name, path + +
+ diff -r 201d8e7dfc43 -r 1a6979fbd544 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jul 21 14:13:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - - - -