Job ID = 1304977 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,003,233 reads read : 22,003,233 reads written : 22,003,233 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:07:18 22003233 reads; of these: 22003233 (100.00%) were unpaired; of these: 401414 (1.82%) aligned 0 times 18946869 (86.11%) aligned exactly 1 time 2654950 (12.07%) aligned >1 times 98.18% overall alignment rate Time searching: 00:07:18 Overall time: 00:07:18 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 9179299 / 21601819 = 0.4249 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, 03 Jun 2019 21:25:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 21:25:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:25:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:25:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 21:25:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:25:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:25:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 21:25:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:25:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:25:56: 1000000 INFO @ Mon, 03 Jun 2019 21:25:56: 1000000 INFO @ Mon, 03 Jun 2019 21:25:57: 1000000 INFO @ Mon, 03 Jun 2019 21:26:05: 2000000 INFO @ Mon, 03 Jun 2019 21:26:05: 2000000 INFO @ Mon, 03 Jun 2019 21:26:07: 2000000 INFO @ Mon, 03 Jun 2019 21:26:15: 3000000 INFO @ Mon, 03 Jun 2019 21:26:15: 3000000 INFO @ Mon, 03 Jun 2019 21:26:17: 3000000 INFO @ Mon, 03 Jun 2019 21:26:24: 4000000 INFO @ Mon, 03 Jun 2019 21:26:25: 4000000 INFO @ Mon, 03 Jun 2019 21:26:27: 4000000 INFO @ Mon, 03 Jun 2019 21:26:33: 5000000 INFO @ Mon, 03 Jun 2019 21:26:34: 5000000 INFO @ Mon, 03 Jun 2019 21:26:37: 5000000 INFO @ Mon, 03 Jun 2019 21:26:43: 6000000 INFO @ Mon, 03 Jun 2019 21:26:44: 6000000 INFO @ Mon, 03 Jun 2019 21:26:47: 6000000 INFO @ Mon, 03 Jun 2019 21:26:52: 7000000 INFO @ Mon, 03 Jun 2019 21:26:53: 7000000 INFO @ Mon, 03 Jun 2019 21:26:57: 7000000 INFO @ Mon, 03 Jun 2019 21:27:02: 8000000 INFO @ Mon, 03 Jun 2019 21:27:03: 8000000 INFO @ Mon, 03 Jun 2019 21:27:07: 8000000 INFO @ Mon, 03 Jun 2019 21:27:11: 9000000 INFO @ Mon, 03 Jun 2019 21:27:12: 9000000 INFO @ Mon, 03 Jun 2019 21:27:17: 9000000 INFO @ Mon, 03 Jun 2019 21:27:20: 10000000 INFO @ Mon, 03 Jun 2019 21:27:22: 10000000 INFO @ Mon, 03 Jun 2019 21:27:27: 10000000 INFO @ Mon, 03 Jun 2019 21:27:29: 11000000 INFO @ Mon, 03 Jun 2019 21:27:31: 11000000 INFO @ Mon, 03 Jun 2019 21:27:37: 11000000 INFO @ Mon, 03 Jun 2019 21:27:38: 12000000 INFO @ Mon, 03 Jun 2019 21:27:41: 12000000 INFO @ Mon, 03 Jun 2019 21:27:42: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:27:42: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:27:42: #1 total tags in treatment: 12422520 INFO @ Mon, 03 Jun 2019 21:27:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:27:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 21:27:42: #1 tags after filtering in treatment: 12422520 INFO @ Mon, 03 Jun 2019 21:27:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:27:42: #1 finished! INFO @ Mon, 03 Jun 2019 21:27:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:27:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:27:43: #2 number of paired peaks: 2735 INFO @ Mon, 03 Jun 2019 21:27:43: start model_add_line... INFO @ Mon, 03 Jun 2019 21:27:44: start X-correlation... INFO @ Mon, 03 Jun 2019 21:27:44: end of X-cor INFO @ Mon, 03 Jun 2019 21:27:44: #2 finished! INFO @ Mon, 03 Jun 2019 21:27:44: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 21:27:44: #2 alternative fragment length(s) may be 2 bps INFO @ Mon, 03 Jun 2019 21:27:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.05_model.r WARNING @ Mon, 03 Jun 2019 21:27:44: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:27:44: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Mon, 03 Jun 2019 21:27:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 21:27:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:27:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:27:45: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:27:45: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:27:45: #1 total tags in treatment: 12422520 INFO @ Mon, 03 Jun 2019 21:27:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:27:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 21:27:46: #1 tags after filtering in treatment: 12422520 INFO @ Mon, 03 Jun 2019 21:27:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:27:46: #1 finished! INFO @ Mon, 03 Jun 2019 21:27:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:27:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:27:47: 12000000 INFO @ Mon, 03 Jun 2019 21:27:47: #2 number of paired peaks: 2735 INFO @ Mon, 03 Jun 2019 21:27:47: start model_add_line... INFO @ Mon, 03 Jun 2019 21:27:47: start X-correlation... INFO @ Mon, 03 Jun 2019 21:27:47: end of X-cor INFO @ Mon, 03 Jun 2019 21:27:47: #2 finished! INFO @ Mon, 03 Jun 2019 21:27:47: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 21:27:47: #2 alternative fragment length(s) may be 2 bps INFO @ Mon, 03 Jun 2019 21:27:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.20_model.r WARNING @ Mon, 03 Jun 2019 21:27:47: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:27:47: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Mon, 03 Jun 2019 21:27:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 21:27:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:27:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:27:51: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 21:27:51: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 21:27:51: #1 total tags in treatment: 12422520 INFO @ Mon, 03 Jun 2019 21:27:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:27:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 21:27:51: #1 tags after filtering in treatment: 12422520 INFO @ Mon, 03 Jun 2019 21:27:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 21:27:51: #1 finished! INFO @ Mon, 03 Jun 2019 21:27:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:27:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:27:53: #2 number of paired peaks: 2735 INFO @ Mon, 03 Jun 2019 21:27:53: start model_add_line... INFO @ Mon, 03 Jun 2019 21:27:53: start X-correlation... INFO @ Mon, 03 Jun 2019 21:27:53: end of X-cor INFO @ Mon, 03 Jun 2019 21:27:53: #2 finished! INFO @ Mon, 03 Jun 2019 21:27:53: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 21:27:53: #2 alternative fragment length(s) may be 2 bps INFO @ Mon, 03 Jun 2019 21:27:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.10_model.r WARNING @ Mon, 03 Jun 2019 21:27:53: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:27:53: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Mon, 03 Jun 2019 21:27:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 21:27:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:27:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:28:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:28:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:28:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:28:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.05_peaks.xls INFO @ Mon, 03 Jun 2019 21:28:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:28:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.05_summits.bed INFO @ Mon, 03 Jun 2019 21:28:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:28:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.20_peaks.xls INFO @ Mon, 03 Jun 2019 21:28:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:28:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.20_summits.bed INFO @ Mon, 03 Jun 2019 21:28:39: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:28:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.10_peaks.xls INFO @ Mon, 03 Jun 2019 21:28:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:28:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495258/SRX495258.10_summits.bed INFO @ Mon, 03 Jun 2019 21:28:44: Done! pass1 - making usageList (0 chroms): 1 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。