Job ID = 2590224 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,874,592 reads read : 57,749,184 reads written : 28,874,592 reads 0-length : 28,874,592 rm: cannot remove ‘[DSE]RR*’: 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: 00:07:35 28874592 reads; of these: 28874592 (100.00%) were unpaired; of these: 2041155 (7.07%) aligned 0 times 22367742 (77.47%) aligned exactly 1 time 4465695 (15.47%) aligned >1 times 92.93% overall alignment rate Time searching: 00:07:35 Overall time: 00:07:35 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_sort_core] merging from 12 files... [bam_rmdupse_core] 5654251 / 26833437 = 0.2107 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 20:29:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.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 20:29:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:29:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:30:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.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 20:30:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:30:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:30:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.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 20:30:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:30:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:30:09: 1000000 INFO @ Mon, 12 Aug 2019 20:30:09: 1000000 INFO @ Mon, 12 Aug 2019 20:30:10: 1000000 INFO @ Mon, 12 Aug 2019 20:30:17: 2000000 INFO @ Mon, 12 Aug 2019 20:30:19: 2000000 INFO @ Mon, 12 Aug 2019 20:30:19: 2000000 INFO @ Mon, 12 Aug 2019 20:30:25: 3000000 INFO @ Mon, 12 Aug 2019 20:30:28: 3000000 INFO @ Mon, 12 Aug 2019 20:30:29: 3000000 INFO @ Mon, 12 Aug 2019 20:30:33: 4000000 INFO @ Mon, 12 Aug 2019 20:30:38: 4000000 INFO @ Mon, 12 Aug 2019 20:30:39: 4000000 INFO @ Mon, 12 Aug 2019 20:30:41: 5000000 INFO @ Mon, 12 Aug 2019 20:30:47: 5000000 INFO @ Mon, 12 Aug 2019 20:30:48: 5000000 INFO @ Mon, 12 Aug 2019 20:30:49: 6000000 INFO @ Mon, 12 Aug 2019 20:30:55: 6000000 INFO @ Mon, 12 Aug 2019 20:30:57: 7000000 INFO @ Mon, 12 Aug 2019 20:30:57: 6000000 INFO @ Mon, 12 Aug 2019 20:31:04: 7000000 INFO @ Mon, 12 Aug 2019 20:31:05: 8000000 INFO @ Mon, 12 Aug 2019 20:31:07: 7000000 INFO @ Mon, 12 Aug 2019 20:31:13: 9000000 INFO @ Mon, 12 Aug 2019 20:31:13: 8000000 INFO @ Mon, 12 Aug 2019 20:31:16: 8000000 INFO @ Mon, 12 Aug 2019 20:31:21: 10000000 INFO @ Mon, 12 Aug 2019 20:31:22: 9000000 INFO @ Mon, 12 Aug 2019 20:31:26: 9000000 INFO @ Mon, 12 Aug 2019 20:31:29: 11000000 INFO @ Mon, 12 Aug 2019 20:31:31: 10000000 INFO @ Mon, 12 Aug 2019 20:31:35: 10000000 INFO @ Mon, 12 Aug 2019 20:31:37: 12000000 INFO @ Mon, 12 Aug 2019 20:31:40: 11000000 INFO @ Mon, 12 Aug 2019 20:31:44: 11000000 INFO @ Mon, 12 Aug 2019 20:31:45: 13000000 INFO @ Mon, 12 Aug 2019 20:31:49: 12000000 INFO @ Mon, 12 Aug 2019 20:31:52: 14000000 INFO @ Mon, 12 Aug 2019 20:31:54: 12000000 INFO @ Mon, 12 Aug 2019 20:31:58: 13000000 INFO @ Mon, 12 Aug 2019 20:32:00: 15000000 INFO @ Mon, 12 Aug 2019 20:32:03: 13000000 INFO @ Mon, 12 Aug 2019 20:32:07: 14000000 INFO @ Mon, 12 Aug 2019 20:32:08: 16000000 INFO @ Mon, 12 Aug 2019 20:32:13: 14000000 INFO @ Mon, 12 Aug 2019 20:32:16: 17000000 INFO @ Mon, 12 Aug 2019 20:32:16: 15000000 INFO @ Mon, 12 Aug 2019 20:32:22: 15000000 INFO @ Mon, 12 Aug 2019 20:32:23: 18000000 INFO @ Mon, 12 Aug 2019 20:32:25: 16000000 INFO @ Mon, 12 Aug 2019 20:32:31: 19000000 INFO @ Mon, 12 Aug 2019 20:32:31: 16000000 INFO @ Mon, 12 Aug 2019 20:32:34: 17000000 INFO @ Mon, 12 Aug 2019 20:32:39: 20000000 INFO @ Mon, 12 Aug 2019 20:32:41: 17000000 INFO @ Mon, 12 Aug 2019 20:32:43: 18000000 INFO @ Mon, 12 Aug 2019 20:32:47: 21000000 INFO @ Mon, 12 Aug 2019 20:32:48: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:32:48: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:32:48: #1 total tags in treatment: 21179186 INFO @ Mon, 12 Aug 2019 20:32:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:32:48: #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 20:32:49: #1 tags after filtering in treatment: 21179186 INFO @ Mon, 12 Aug 2019 20:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:32:49: #1 finished! INFO @ Mon, 12 Aug 2019 20:32:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:32:50: #2 number of paired peaks: 221 WARNING @ Mon, 12 Aug 2019 20:32:50: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Mon, 12 Aug 2019 20:32:50: start model_add_line... INFO @ Mon, 12 Aug 2019 20:32:51: 18000000 INFO @ Mon, 12 Aug 2019 20:32:51: start X-correlation... INFO @ Mon, 12 Aug 2019 20:32:51: end of X-cor INFO @ Mon, 12 Aug 2019 20:32:51: #2 finished! INFO @ Mon, 12 Aug 2019 20:32:51: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:32:51: #2 alternative fragment length(s) may be 1,12 bps INFO @ Mon, 12 Aug 2019 20:32:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.10_model.r WARNING @ Mon, 12 Aug 2019 20:32:51: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:32:51: #2 You may need to consider one of the other alternative d(s): 1,12 WARNING @ Mon, 12 Aug 2019 20:32:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:32:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:32:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:32:51: 19000000 INFO @ Mon, 12 Aug 2019 20:33:00: 20000000 INFO @ Mon, 12 Aug 2019 20:33:00: 19000000 INFO @ Mon, 12 Aug 2019 20:33:09: 21000000 INFO @ Mon, 12 Aug 2019 20:33:10: 20000000 INFO @ Mon, 12 Aug 2019 20:33:11: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:33:11: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:33:11: #1 total tags in treatment: 21179186 INFO @ Mon, 12 Aug 2019 20:33:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:33:11: #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 20:33:11: #1 tags after filtering in treatment: 21179186 INFO @ Mon, 12 Aug 2019 20:33:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:33:11: #1 finished! INFO @ Mon, 12 Aug 2019 20:33:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:33:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:33:13: #2 number of paired peaks: 221 WARNING @ Mon, 12 Aug 2019 20:33:13: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Mon, 12 Aug 2019 20:33:13: start model_add_line... INFO @ Mon, 12 Aug 2019 20:33:13: start X-correlation... INFO @ Mon, 12 Aug 2019 20:33:13: end of X-cor INFO @ Mon, 12 Aug 2019 20:33:13: #2 finished! INFO @ Mon, 12 Aug 2019 20:33:13: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:33:13: #2 alternative fragment length(s) may be 1,12 bps INFO @ Mon, 12 Aug 2019 20:33:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.20_model.r WARNING @ Mon, 12 Aug 2019 20:33:13: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:33:13: #2 You may need to consider one of the other alternative d(s): 1,12 WARNING @ Mon, 12 Aug 2019 20:33:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:33:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:33:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:33:19: 21000000 INFO @ Mon, 12 Aug 2019 20:33:21: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:33:21: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:33:21: #1 total tags in treatment: 21179186 INFO @ Mon, 12 Aug 2019 20:33:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:33:21: #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 20:33:21: #1 tags after filtering in treatment: 21179186 INFO @ Mon, 12 Aug 2019 20:33:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:33:21: #1 finished! INFO @ Mon, 12 Aug 2019 20:33:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:33:23: #2 number of paired peaks: 221 WARNING @ Mon, 12 Aug 2019 20:33:23: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Mon, 12 Aug 2019 20:33:23: start model_add_line... INFO @ Mon, 12 Aug 2019 20:33:23: start X-correlation... INFO @ Mon, 12 Aug 2019 20:33:23: end of X-cor INFO @ Mon, 12 Aug 2019 20:33:23: #2 finished! INFO @ Mon, 12 Aug 2019 20:33:23: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:33:23: #2 alternative fragment length(s) may be 1,12 bps INFO @ Mon, 12 Aug 2019 20:33:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.05_model.r WARNING @ Mon, 12 Aug 2019 20:33:23: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:33:23: #2 You may need to consider one of the other alternative d(s): 1,12 WARNING @ Mon, 12 Aug 2019 20:33:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:33:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:33:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:33:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:33:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:33:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:33:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.10_summits.bed INFO @ Mon, 12 Aug 2019 20:33:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:33:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:34:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:34:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:34:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:34:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.20_summits.bed INFO @ Mon, 12 Aug 2019 20:34:18: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:34:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:34:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:34:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709765/SRX5709765.05_summits.bed INFO @ Mon, 12 Aug 2019 20:34:29: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。