Job ID = 1293278 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,379,734 reads read : 25,379,734 reads written : 25,379,734 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: 00:03:45 25379734 reads; of these: 25379734 (100.00%) were unpaired; of these: 584612 (2.30%) aligned 0 times 23238749 (91.56%) aligned exactly 1 time 1556373 (6.13%) aligned >1 times 97.70% overall alignment rate Time searching: 00:03:45 Overall time: 00:03:45 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] 9756366 / 24795122 = 0.3935 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 @ Sun, 02 Jun 2019 22:53:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.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 @ Sun, 02 Jun 2019 22:53:16: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:53:16: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:53:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.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 @ Sun, 02 Jun 2019 22:53:16: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:53:16: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:53:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.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 @ Sun, 02 Jun 2019 22:53:16: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:53:16: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:53:22: 1000000 INFO @ Sun, 02 Jun 2019 22:53:23: 1000000 INFO @ Sun, 02 Jun 2019 22:53:24: 1000000 INFO @ Sun, 02 Jun 2019 22:53:28: 2000000 INFO @ Sun, 02 Jun 2019 22:53:29: 2000000 INFO @ Sun, 02 Jun 2019 22:53:31: 2000000 INFO @ Sun, 02 Jun 2019 22:53:34: 3000000 INFO @ Sun, 02 Jun 2019 22:53:35: 3000000 INFO @ Sun, 02 Jun 2019 22:53:37: 3000000 INFO @ Sun, 02 Jun 2019 22:53:39: 4000000 INFO @ Sun, 02 Jun 2019 22:53:41: 4000000 INFO @ Sun, 02 Jun 2019 22:53:43: 4000000 INFO @ Sun, 02 Jun 2019 22:53:45: 5000000 INFO @ Sun, 02 Jun 2019 22:53:47: 5000000 INFO @ Sun, 02 Jun 2019 22:53:49: 5000000 INFO @ Sun, 02 Jun 2019 22:53:51: 6000000 INFO @ Sun, 02 Jun 2019 22:53:53: 6000000 INFO @ Sun, 02 Jun 2019 22:53:55: 6000000 INFO @ Sun, 02 Jun 2019 22:53:57: 7000000 INFO @ Sun, 02 Jun 2019 22:54:00: 7000000 INFO @ Sun, 02 Jun 2019 22:54:02: 7000000 INFO @ Sun, 02 Jun 2019 22:54:03: 8000000 INFO @ Sun, 02 Jun 2019 22:54:06: 8000000 INFO @ Sun, 02 Jun 2019 22:54:08: 8000000 INFO @ Sun, 02 Jun 2019 22:54:09: 9000000 INFO @ Sun, 02 Jun 2019 22:54:13: 9000000 INFO @ Sun, 02 Jun 2019 22:54:14: 9000000 INFO @ Sun, 02 Jun 2019 22:54:15: 10000000 INFO @ Sun, 02 Jun 2019 22:54:19: 10000000 INFO @ Sun, 02 Jun 2019 22:54:20: 10000000 INFO @ Sun, 02 Jun 2019 22:54:20: 11000000 INFO @ Sun, 02 Jun 2019 22:54:25: 11000000 INFO @ Sun, 02 Jun 2019 22:54:26: 12000000 INFO @ Sun, 02 Jun 2019 22:54:27: 11000000 INFO @ Sun, 02 Jun 2019 22:54:32: 12000000 INFO @ Sun, 02 Jun 2019 22:54:33: 13000000 INFO @ Sun, 02 Jun 2019 22:54:33: 12000000 INFO @ Sun, 02 Jun 2019 22:54:38: 13000000 INFO @ Sun, 02 Jun 2019 22:54:38: 14000000 INFO @ Sun, 02 Jun 2019 22:54:40: 13000000 INFO @ Sun, 02 Jun 2019 22:54:44: 15000000 INFO @ Sun, 02 Jun 2019 22:54:44: 14000000 INFO @ Sun, 02 Jun 2019 22:54:45: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:54:45: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:54:45: #1 total tags in treatment: 15038756 INFO @ Sun, 02 Jun 2019 22:54:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:54:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:54:45: #1 tags after filtering in treatment: 15038756 INFO @ Sun, 02 Jun 2019 22:54:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:54:45: #1 finished! INFO @ Sun, 02 Jun 2019 22:54:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:54:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:54:46: 14000000 INFO @ Sun, 02 Jun 2019 22:54:48: #2 number of paired peaks: 15067 INFO @ Sun, 02 Jun 2019 22:54:48: start model_add_line... INFO @ Sun, 02 Jun 2019 22:54:49: start X-correlation... INFO @ Sun, 02 Jun 2019 22:54:49: end of X-cor INFO @ Sun, 02 Jun 2019 22:54:49: #2 finished! INFO @ Sun, 02 Jun 2019 22:54:49: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 22:54:49: #2 alternative fragment length(s) may be 2,59 bps INFO @ Sun, 02 Jun 2019 22:54:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.05_model.r WARNING @ Sun, 02 Jun 2019 22:54:49: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:54:49: #2 You may need to consider one of the other alternative d(s): 2,59 WARNING @ Sun, 02 Jun 2019 22:54:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:54:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:54:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:54:51: 15000000 INFO @ Sun, 02 Jun 2019 22:54:51: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:54:51: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:54:51: #1 total tags in treatment: 15038756 INFO @ Sun, 02 Jun 2019 22:54:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:54:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:54:51: #1 tags after filtering in treatment: 15038756 INFO @ Sun, 02 Jun 2019 22:54:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:54:51: #1 finished! INFO @ Sun, 02 Jun 2019 22:54:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:54:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:54:52: 15000000 INFO @ Sun, 02 Jun 2019 22:54:53: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:54:53: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:54:53: #1 total tags in treatment: 15038756 INFO @ Sun, 02 Jun 2019 22:54:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:54:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:54:53: #1 tags after filtering in treatment: 15038756 INFO @ Sun, 02 Jun 2019 22:54:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:54:53: #1 finished! INFO @ Sun, 02 Jun 2019 22:54:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:54:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:54:55: #2 number of paired peaks: 15067 INFO @ Sun, 02 Jun 2019 22:54:55: start model_add_line... INFO @ Sun, 02 Jun 2019 22:54:55: start X-correlation... INFO @ Sun, 02 Jun 2019 22:54:55: end of X-cor INFO @ Sun, 02 Jun 2019 22:54:55: #2 finished! INFO @ Sun, 02 Jun 2019 22:54:55: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 22:54:55: #2 alternative fragment length(s) may be 2,59 bps INFO @ Sun, 02 Jun 2019 22:54:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.20_model.r WARNING @ Sun, 02 Jun 2019 22:54:55: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:54:55: #2 You may need to consider one of the other alternative d(s): 2,59 WARNING @ Sun, 02 Jun 2019 22:54:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:54:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:54:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:54:56: #2 number of paired peaks: 15067 INFO @ Sun, 02 Jun 2019 22:54:56: start model_add_line... INFO @ Sun, 02 Jun 2019 22:54:57: start X-correlation... INFO @ Sun, 02 Jun 2019 22:54:57: end of X-cor INFO @ Sun, 02 Jun 2019 22:54:57: #2 finished! INFO @ Sun, 02 Jun 2019 22:54:57: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 22:54:57: #2 alternative fragment length(s) may be 2,59 bps INFO @ Sun, 02 Jun 2019 22:54:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.10_model.r WARNING @ Sun, 02 Jun 2019 22:54:57: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:54:57: #2 You may need to consider one of the other alternative d(s): 2,59 WARNING @ Sun, 02 Jun 2019 22:54:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:54:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:54:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:55:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:55:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:55:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:55:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:55:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:55:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.05_summits.bed INFO @ Sun, 02 Jun 2019 22:55:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:55:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:55:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:55:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.20_summits.bed INFO @ Sun, 02 Jun 2019 22:55:36: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:55:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:55:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:55:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011416/ERX011416.10_summits.bed INFO @ Sun, 02 Jun 2019 22:55:38: 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。