Job ID = 2590259 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,089,738 reads read : 34,089,738 reads written : 34,089,738 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR100228.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: 00:11:44 34089738 reads; of these: 34089738 (100.00%) were unpaired; of these: 4366949 (12.81%) aligned 0 times 27890727 (81.82%) aligned exactly 1 time 1832062 (5.37%) aligned >1 times 87.19% overall alignment rate Time searching: 00:11:44 Overall time: 00:11:45 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 16 files... [bam_rmdupse_core] 13079947 / 29722789 = 0.4401 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 20:41:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.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 20:41:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:41:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:41:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.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 20:41:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:41:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:41:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.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 20:41:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:41:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:41:46: 1000000 INFO @ Mon, 12 Aug 2019 20:41:47: 1000000 INFO @ Mon, 12 Aug 2019 20:41:48: 1000000 INFO @ Mon, 12 Aug 2019 20:41:56: 2000000 INFO @ Mon, 12 Aug 2019 20:41:57: 2000000 INFO @ Mon, 12 Aug 2019 20:41:57: 2000000 INFO @ Mon, 12 Aug 2019 20:42:05: 3000000 INFO @ Mon, 12 Aug 2019 20:42:06: 3000000 INFO @ Mon, 12 Aug 2019 20:42:06: 3000000 INFO @ Mon, 12 Aug 2019 20:42:14: 4000000 INFO @ Mon, 12 Aug 2019 20:42:15: 4000000 INFO @ Mon, 12 Aug 2019 20:42:15: 4000000 INFO @ Mon, 12 Aug 2019 20:42:23: 5000000 INFO @ Mon, 12 Aug 2019 20:42:24: 5000000 INFO @ Mon, 12 Aug 2019 20:42:24: 5000000 INFO @ Mon, 12 Aug 2019 20:42:32: 6000000 INFO @ Mon, 12 Aug 2019 20:42:32: 6000000 INFO @ Mon, 12 Aug 2019 20:42:33: 6000000 INFO @ Mon, 12 Aug 2019 20:42:40: 7000000 INFO @ Mon, 12 Aug 2019 20:42:40: 7000000 INFO @ Mon, 12 Aug 2019 20:42:41: 7000000 INFO @ Mon, 12 Aug 2019 20:42:48: 8000000 INFO @ Mon, 12 Aug 2019 20:42:49: 8000000 INFO @ Mon, 12 Aug 2019 20:42:50: 8000000 INFO @ Mon, 12 Aug 2019 20:42:56: 9000000 INFO @ Mon, 12 Aug 2019 20:42:57: 9000000 INFO @ Mon, 12 Aug 2019 20:42:58: 9000000 INFO @ Mon, 12 Aug 2019 20:43:03: 10000000 INFO @ Mon, 12 Aug 2019 20:43:06: 10000000 INFO @ Mon, 12 Aug 2019 20:43:06: 10000000 INFO @ Mon, 12 Aug 2019 20:43:11: 11000000 INFO @ Mon, 12 Aug 2019 20:43:14: 11000000 INFO @ Mon, 12 Aug 2019 20:43:15: 11000000 INFO @ Mon, 12 Aug 2019 20:43:19: 12000000 INFO @ Mon, 12 Aug 2019 20:43:23: 12000000 INFO @ Mon, 12 Aug 2019 20:43:23: 12000000 INFO @ Mon, 12 Aug 2019 20:43:26: 13000000 INFO @ Mon, 12 Aug 2019 20:43:31: 13000000 INFO @ Mon, 12 Aug 2019 20:43:31: 13000000 INFO @ Mon, 12 Aug 2019 20:43:34: 14000000 INFO @ Mon, 12 Aug 2019 20:43:40: 14000000 INFO @ Mon, 12 Aug 2019 20:43:40: 14000000 INFO @ Mon, 12 Aug 2019 20:43:42: 15000000 INFO @ Mon, 12 Aug 2019 20:43:48: 15000000 INFO @ Mon, 12 Aug 2019 20:43:49: 15000000 INFO @ Mon, 12 Aug 2019 20:43:50: 16000000 INFO @ Mon, 12 Aug 2019 20:43:55: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:43:55: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:43:55: #1 total tags in treatment: 16642842 INFO @ Mon, 12 Aug 2019 20:43:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:43:55: #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 20:43:55: #1 tags after filtering in treatment: 16642842 INFO @ Mon, 12 Aug 2019 20:43:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:43:55: #1 finished! INFO @ Mon, 12 Aug 2019 20:43:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:43:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:43:57: #2 number of paired peaks: 2868 INFO @ Mon, 12 Aug 2019 20:43:57: start model_add_line... INFO @ Mon, 12 Aug 2019 20:43:58: start X-correlation... INFO @ Mon, 12 Aug 2019 20:43:58: end of X-cor INFO @ Mon, 12 Aug 2019 20:43:58: #2 finished! INFO @ Mon, 12 Aug 2019 20:43:58: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:43:58: #2 alternative fragment length(s) may be 1 bps INFO @ Mon, 12 Aug 2019 20:43:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.20_model.r INFO @ Mon, 12 Aug 2019 20:43:58: 16000000 WARNING @ Mon, 12 Aug 2019 20:43:58: #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 20:43:58: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Mon, 12 Aug 2019 20:43:58: #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 20:43:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:43:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:43:58: 16000000 INFO @ Mon, 12 Aug 2019 20:44:04: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:44:04: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:44:04: #1 total tags in treatment: 16642842 INFO @ Mon, 12 Aug 2019 20:44:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:44:04: #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 20:44:04: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:44:04: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:44:04: #1 total tags in treatment: 16642842 INFO @ Mon, 12 Aug 2019 20:44:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:44:04: #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 20:44:04: #1 tags after filtering in treatment: 16642842 INFO @ Mon, 12 Aug 2019 20:44:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:44:04: #1 finished! INFO @ Mon, 12 Aug 2019 20:44:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:44:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:44:04: #1 tags after filtering in treatment: 16642842 INFO @ Mon, 12 Aug 2019 20:44:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:44:04: #1 finished! INFO @ Mon, 12 Aug 2019 20:44:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:44:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:44:06: #2 number of paired peaks: 2868 INFO @ Mon, 12 Aug 2019 20:44:06: start model_add_line... INFO @ Mon, 12 Aug 2019 20:44:06: #2 number of paired peaks: 2868 INFO @ Mon, 12 Aug 2019 20:44:06: start model_add_line... INFO @ Mon, 12 Aug 2019 20:44:06: start X-correlation... INFO @ Mon, 12 Aug 2019 20:44:06: end of X-cor INFO @ Mon, 12 Aug 2019 20:44:06: #2 finished! INFO @ Mon, 12 Aug 2019 20:44:06: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:44:06: #2 alternative fragment length(s) may be 1 bps INFO @ Mon, 12 Aug 2019 20:44:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.05_model.r WARNING @ Mon, 12 Aug 2019 20:44:06: #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 20:44:06: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Mon, 12 Aug 2019 20:44:06: #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 20:44:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:44:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:44:07: start X-correlation... INFO @ Mon, 12 Aug 2019 20:44:07: end of X-cor INFO @ Mon, 12 Aug 2019 20:44:07: #2 finished! INFO @ Mon, 12 Aug 2019 20:44:07: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:44:07: #2 alternative fragment length(s) may be 1 bps INFO @ Mon, 12 Aug 2019 20:44:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.10_model.r WARNING @ Mon, 12 Aug 2019 20:44:07: #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 20:44:07: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Mon, 12 Aug 2019 20:44:07: #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 20:44:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:44:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:44:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:44:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:44:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:44:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:44:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:44:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.20_summits.bed INFO @ Mon, 12 Aug 2019 20:44:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.10_summits.bed INFO @ Mon, 12 Aug 2019 20:44:55: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX042247/SRX042247.05_summits.bed INFO @ Mon, 12 Aug 2019 20:44:55: 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。