Job ID = 2589115 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,488,173 reads read : 7,488,173 reads written : 7,488,173 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107299.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:11 7488173 reads; of these: 7488173 (100.00%) were unpaired; of these: 701264 (9.36%) aligned 0 times 6048411 (80.77%) aligned exactly 1 time 738498 (9.86%) aligned >1 times 90.64% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1126211 / 6786909 = 0.1659 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 16:58:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 16:58:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:58:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 16:58:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 16:58:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:58:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 16:58:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 16:58:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:58:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 16:58:25: 1000000 INFO @ Mon, 12 Aug 2019 16:58:26: 1000000 INFO @ Mon, 12 Aug 2019 16:58:26: 1000000 INFO @ Mon, 12 Aug 2019 16:58:32: 2000000 INFO @ Mon, 12 Aug 2019 16:58:33: 2000000 INFO @ Mon, 12 Aug 2019 16:58:34: 2000000 INFO @ Mon, 12 Aug 2019 16:58:39: 3000000 INFO @ Mon, 12 Aug 2019 16:58:40: 3000000 INFO @ Mon, 12 Aug 2019 16:58:41: 3000000 INFO @ Mon, 12 Aug 2019 16:58:47: 4000000 INFO @ Mon, 12 Aug 2019 16:58:48: 4000000 INFO @ Mon, 12 Aug 2019 16:58:48: 4000000 INFO @ Mon, 12 Aug 2019 16:58:54: 5000000 INFO @ Mon, 12 Aug 2019 16:58:55: 5000000 INFO @ Mon, 12 Aug 2019 16:58:56: 5000000 INFO @ Mon, 12 Aug 2019 16:58:59: #1 tag size is determined as 27 bps INFO @ Mon, 12 Aug 2019 16:58:59: #1 tag size = 27 INFO @ Mon, 12 Aug 2019 16:58:59: #1 total tags in treatment: 5660698 INFO @ Mon, 12 Aug 2019 16:58:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 16:58:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 16:58:59: #1 tags after filtering in treatment: 5660698 INFO @ Mon, 12 Aug 2019 16:58:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 16:58:59: #1 finished! INFO @ Mon, 12 Aug 2019 16:58:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 16:58:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 16:59:00: #2 number of paired peaks: 1513 INFO @ Mon, 12 Aug 2019 16:59:00: start model_add_line... INFO @ Mon, 12 Aug 2019 16:59:00: start X-correlation... INFO @ Mon, 12 Aug 2019 16:59:00: end of X-cor INFO @ Mon, 12 Aug 2019 16:59:00: #2 finished! INFO @ Mon, 12 Aug 2019 16:59:00: #2 predicted fragment length is 146 bps INFO @ Mon, 12 Aug 2019 16:59:00: #2 alternative fragment length(s) may be 146 bps INFO @ Mon, 12 Aug 2019 16:59:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.05_model.r INFO @ Mon, 12 Aug 2019 16:59:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 16:59:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 16:59:00: #1 tag size is determined as 27 bps INFO @ Mon, 12 Aug 2019 16:59:00: #1 tag size = 27 INFO @ Mon, 12 Aug 2019 16:59:00: #1 total tags in treatment: 5660698 INFO @ Mon, 12 Aug 2019 16:59:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 16:59:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 16:59:00: #1 tags after filtering in treatment: 5660698 INFO @ Mon, 12 Aug 2019 16:59:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 16:59:00: #1 finished! INFO @ Mon, 12 Aug 2019 16:59:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 16:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 16:59:00: #1 tag size is determined as 27 bps INFO @ Mon, 12 Aug 2019 16:59:00: #1 tag size = 27 INFO @ Mon, 12 Aug 2019 16:59:00: #1 total tags in treatment: 5660698 INFO @ Mon, 12 Aug 2019 16:59:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 16:59:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 16:59:01: #1 tags after filtering in treatment: 5660698 INFO @ Mon, 12 Aug 2019 16:59:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 16:59:01: #1 finished! INFO @ Mon, 12 Aug 2019 16:59:01: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 16:59:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 16:59:01: #2 number of paired peaks: 1513 INFO @ Mon, 12 Aug 2019 16:59:01: start model_add_line... INFO @ Mon, 12 Aug 2019 16:59:01: start X-correlation... INFO @ Mon, 12 Aug 2019 16:59:01: end of X-cor INFO @ Mon, 12 Aug 2019 16:59:01: #2 finished! INFO @ Mon, 12 Aug 2019 16:59:01: #2 predicted fragment length is 146 bps INFO @ Mon, 12 Aug 2019 16:59:01: #2 alternative fragment length(s) may be 146 bps INFO @ Mon, 12 Aug 2019 16:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.10_model.r INFO @ Mon, 12 Aug 2019 16:59:01: #3 Call peaks... INFO @ Mon, 12 Aug 2019 16:59:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 16:59:01: #2 number of paired peaks: 1513 INFO @ Mon, 12 Aug 2019 16:59:01: start model_add_line... INFO @ Mon, 12 Aug 2019 16:59:01: start X-correlation... INFO @ Mon, 12 Aug 2019 16:59:01: end of X-cor INFO @ Mon, 12 Aug 2019 16:59:01: #2 finished! INFO @ Mon, 12 Aug 2019 16:59:01: #2 predicted fragment length is 146 bps INFO @ Mon, 12 Aug 2019 16:59:01: #2 alternative fragment length(s) may be 146 bps INFO @ Mon, 12 Aug 2019 16:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.20_model.r INFO @ Mon, 12 Aug 2019 16:59:01: #3 Call peaks... INFO @ Mon, 12 Aug 2019 16:59:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 16:59:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 16:59:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 16:59:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 16:59:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.05_peaks.xls INFO @ Mon, 12 Aug 2019 16:59:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 16:59:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.05_summits.bed INFO @ Mon, 12 Aug 2019 16:59:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3473 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 16:59:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.10_peaks.xls INFO @ Mon, 12 Aug 2019 16:59:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 16:59:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.10_summits.bed INFO @ Mon, 12 Aug 2019 16:59:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1472 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 16:59:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.20_peaks.xls INFO @ Mon, 12 Aug 2019 16:59:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 16:59:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043844/SRX043844.20_summits.bed INFO @ Mon, 12 Aug 2019 16:59:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (371 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。