Job ID = 2590265 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,506,893 reads read : 27,506,893 reads written : 27,506,893 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR139078.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:56 27506893 reads; of these: 27506893 (100.00%) were unpaired; of these: 1209210 (4.40%) aligned 0 times 17434208 (63.38%) aligned exactly 1 time 8863475 (32.22%) aligned >1 times 95.60% overall alignment rate Time searching: 00:09:57 Overall time: 00:09:57 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] 10402206 / 26297683 = 0.3956 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 20:34:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.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, 12 Aug 2019 20:34:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:34:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:34:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.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, 12 Aug 2019 20:34:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:34:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:34:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.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, 12 Aug 2019 20:34:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:34:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:34:23: 1000000 INFO @ Mon, 12 Aug 2019 20:34:24: 1000000 INFO @ Mon, 12 Aug 2019 20:34:25: 1000000 INFO @ Mon, 12 Aug 2019 20:34:30: 2000000 INFO @ Mon, 12 Aug 2019 20:34:30: 2000000 INFO @ Mon, 12 Aug 2019 20:34:32: 2000000 INFO @ Mon, 12 Aug 2019 20:34:36: 3000000 INFO @ Mon, 12 Aug 2019 20:34:37: 3000000 INFO @ Mon, 12 Aug 2019 20:34:38: 3000000 INFO @ Mon, 12 Aug 2019 20:34:42: 4000000 INFO @ Mon, 12 Aug 2019 20:34:43: 4000000 INFO @ Mon, 12 Aug 2019 20:34:45: 4000000 INFO @ Mon, 12 Aug 2019 20:34:49: 5000000 INFO @ Mon, 12 Aug 2019 20:34:50: 5000000 INFO @ Mon, 12 Aug 2019 20:34:51: 5000000 INFO @ Mon, 12 Aug 2019 20:34:57: 6000000 INFO @ Mon, 12 Aug 2019 20:34:57: 6000000 INFO @ Mon, 12 Aug 2019 20:34:58: 6000000 INFO @ Mon, 12 Aug 2019 20:35:05: 7000000 INFO @ Mon, 12 Aug 2019 20:35:05: 7000000 INFO @ Mon, 12 Aug 2019 20:35:05: 7000000 INFO @ Mon, 12 Aug 2019 20:35:11: 8000000 INFO @ Mon, 12 Aug 2019 20:35:11: 8000000 INFO @ Mon, 12 Aug 2019 20:35:12: 8000000 INFO @ Mon, 12 Aug 2019 20:35:17: 9000000 INFO @ Mon, 12 Aug 2019 20:35:18: 9000000 INFO @ Mon, 12 Aug 2019 20:35:19: 9000000 INFO @ Mon, 12 Aug 2019 20:35:23: 10000000 INFO @ Mon, 12 Aug 2019 20:35:25: 10000000 INFO @ Mon, 12 Aug 2019 20:35:25: 10000000 INFO @ Mon, 12 Aug 2019 20:35:30: 11000000 INFO @ Mon, 12 Aug 2019 20:35:32: 11000000 INFO @ Mon, 12 Aug 2019 20:35:32: 11000000 INFO @ Mon, 12 Aug 2019 20:35:36: 12000000 INFO @ Mon, 12 Aug 2019 20:35:38: 12000000 INFO @ Mon, 12 Aug 2019 20:35:39: 12000000 INFO @ Mon, 12 Aug 2019 20:35:42: 13000000 INFO @ Mon, 12 Aug 2019 20:35:45: 13000000 INFO @ Mon, 12 Aug 2019 20:35:46: 13000000 INFO @ Mon, 12 Aug 2019 20:35:48: 14000000 INFO @ Mon, 12 Aug 2019 20:35:52: 14000000 INFO @ Mon, 12 Aug 2019 20:35:53: 14000000 INFO @ Mon, 12 Aug 2019 20:35:54: 15000000 INFO @ Mon, 12 Aug 2019 20:35:59: 15000000 INFO @ Mon, 12 Aug 2019 20:35:59: 15000000 INFO @ Mon, 12 Aug 2019 20:36:00: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:36:00: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:36:00: #1 total tags in treatment: 15895477 INFO @ Mon, 12 Aug 2019 20:36:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:36:00: #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 20:36:01: #1 tags after filtering in treatment: 15895477 INFO @ Mon, 12 Aug 2019 20:36:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:36:01: #1 finished! INFO @ Mon, 12 Aug 2019 20:36:01: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:36:02: #2 number of paired peaks: 1439 INFO @ Mon, 12 Aug 2019 20:36:02: start model_add_line... INFO @ Mon, 12 Aug 2019 20:36:02: start X-correlation... INFO @ Mon, 12 Aug 2019 20:36:02: end of X-cor INFO @ Mon, 12 Aug 2019 20:36:02: #2 finished! INFO @ Mon, 12 Aug 2019 20:36:02: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 20:36:02: #2 alternative fragment length(s) may be 2,35,560 bps INFO @ Mon, 12 Aug 2019 20:36:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.10_model.r WARNING @ Mon, 12 Aug 2019 20:36:02: #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, 12 Aug 2019 20:36:02: #2 You may need to consider one of the other alternative d(s): 2,35,560 WARNING @ Mon, 12 Aug 2019 20:36:02: #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 20:36:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:36:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:36:05: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:36:05: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:36:05: #1 total tags in treatment: 15895477 INFO @ Mon, 12 Aug 2019 20:36:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:36:05: #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 20:36:05: #1 tags after filtering in treatment: 15895477 INFO @ Mon, 12 Aug 2019 20:36:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:36:05: #1 finished! INFO @ Mon, 12 Aug 2019 20:36:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:36:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:36:06: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:36:06: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:36:06: #1 total tags in treatment: 15895477 INFO @ Mon, 12 Aug 2019 20:36:06: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:36:06: #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 20:36:06: #1 tags after filtering in treatment: 15895477 INFO @ Mon, 12 Aug 2019 20:36:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:36:06: #1 finished! INFO @ Mon, 12 Aug 2019 20:36:06: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:36:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:36:07: #2 number of paired peaks: 1439 INFO @ Mon, 12 Aug 2019 20:36:07: start model_add_line... INFO @ Mon, 12 Aug 2019 20:36:07: start X-correlation... INFO @ Mon, 12 Aug 2019 20:36:07: end of X-cor INFO @ Mon, 12 Aug 2019 20:36:07: #2 finished! INFO @ Mon, 12 Aug 2019 20:36:07: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 20:36:07: #2 alternative fragment length(s) may be 2,35,560 bps INFO @ Mon, 12 Aug 2019 20:36:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.05_model.r WARNING @ Mon, 12 Aug 2019 20:36:07: #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, 12 Aug 2019 20:36:07: #2 You may need to consider one of the other alternative d(s): 2,35,560 WARNING @ Mon, 12 Aug 2019 20:36:07: #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 20:36:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:36:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:36:07: #2 number of paired peaks: 1439 INFO @ Mon, 12 Aug 2019 20:36:07: start model_add_line... INFO @ Mon, 12 Aug 2019 20:36:08: start X-correlation... INFO @ Mon, 12 Aug 2019 20:36:08: end of X-cor INFO @ Mon, 12 Aug 2019 20:36:08: #2 finished! INFO @ Mon, 12 Aug 2019 20:36:08: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 20:36:08: #2 alternative fragment length(s) may be 2,35,560 bps INFO @ Mon, 12 Aug 2019 20:36:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.20_model.r WARNING @ Mon, 12 Aug 2019 20:36:08: #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, 12 Aug 2019 20:36:08: #2 You may need to consider one of the other alternative d(s): 2,35,560 WARNING @ Mon, 12 Aug 2019 20:36:08: #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 20:36:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:36:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:36:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:36:47: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:36:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:37:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:37:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.10_summits.bed INFO @ Mon, 12 Aug 2019 20:37:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:37:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:37:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:37:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.05_summits.bed INFO @ Mon, 12 Aug 2019 20:37:05: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:37:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:37:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:37:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX050596/SRX050596.20_summits.bed INFO @ Mon, 12 Aug 2019 20:37:06: 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。