Job ID = 1293782 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,984,833 reads read : 22,984,833 reads written : 22,984,833 spots read : 22,005,854 reads read : 22,005,854 reads written : 22,005,854 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: 00:09:40 44990687 reads; of these: 44990687 (100.00%) were unpaired; of these: 3947980 (8.78%) aligned 0 times 37875265 (84.18%) aligned exactly 1 time 3167442 (7.04%) aligned >1 times 91.22% overall alignment rate Time searching: 00:09:40 Overall time: 00:09:40 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 12 files... [bam_rmdupse_core] 20625858 / 41042707 = 0.5025 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 02:51:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.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 02:51:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:51:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:51:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.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 02:51:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:51:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:51:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.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 02:51:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:51:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:51:47: 1000000 INFO @ Mon, 03 Jun 2019 02:51:47: 1000000 INFO @ Mon, 03 Jun 2019 02:51:48: 1000000 INFO @ Mon, 03 Jun 2019 02:51:56: 2000000 INFO @ Mon, 03 Jun 2019 02:51:57: 2000000 INFO @ Mon, 03 Jun 2019 02:51:58: 2000000 INFO @ Mon, 03 Jun 2019 02:52:05: 3000000 INFO @ Mon, 03 Jun 2019 02:52:06: 3000000 INFO @ Mon, 03 Jun 2019 02:52:08: 3000000 INFO @ Mon, 03 Jun 2019 02:52:13: 4000000 INFO @ Mon, 03 Jun 2019 02:52:15: 4000000 INFO @ Mon, 03 Jun 2019 02:52:18: 4000000 INFO @ Mon, 03 Jun 2019 02:52:22: 5000000 INFO @ Mon, 03 Jun 2019 02:52:24: 5000000 INFO @ Mon, 03 Jun 2019 02:52:27: 5000000 INFO @ Mon, 03 Jun 2019 02:52:30: 6000000 INFO @ Mon, 03 Jun 2019 02:52:33: 6000000 INFO @ Mon, 03 Jun 2019 02:52:37: 6000000 INFO @ Mon, 03 Jun 2019 02:52:39: 7000000 INFO @ Mon, 03 Jun 2019 02:52:41: 7000000 INFO @ Mon, 03 Jun 2019 02:52:46: 7000000 INFO @ Mon, 03 Jun 2019 02:52:47: 8000000 INFO @ Mon, 03 Jun 2019 02:52:50: 8000000 INFO @ Mon, 03 Jun 2019 02:52:55: 8000000 INFO @ Mon, 03 Jun 2019 02:52:56: 9000000 INFO @ Mon, 03 Jun 2019 02:52:59: 9000000 INFO @ Mon, 03 Jun 2019 02:53:04: 10000000 INFO @ Mon, 03 Jun 2019 02:53:05: 9000000 INFO @ Mon, 03 Jun 2019 02:53:07: 10000000 INFO @ Mon, 03 Jun 2019 02:53:12: 11000000 INFO @ Mon, 03 Jun 2019 02:53:14: 10000000 INFO @ Mon, 03 Jun 2019 02:53:16: 11000000 INFO @ Mon, 03 Jun 2019 02:53:21: 12000000 INFO @ Mon, 03 Jun 2019 02:53:23: 11000000 INFO @ Mon, 03 Jun 2019 02:53:25: 12000000 INFO @ Mon, 03 Jun 2019 02:53:29: 13000000 INFO @ Mon, 03 Jun 2019 02:53:32: 12000000 INFO @ Mon, 03 Jun 2019 02:53:33: 13000000 INFO @ Mon, 03 Jun 2019 02:53:37: 14000000 INFO @ Mon, 03 Jun 2019 02:53:42: 13000000 INFO @ Mon, 03 Jun 2019 02:53:42: 14000000 INFO @ Mon, 03 Jun 2019 02:53:46: 15000000 INFO @ Mon, 03 Jun 2019 02:53:50: 15000000 INFO @ Mon, 03 Jun 2019 02:53:51: 14000000 INFO @ Mon, 03 Jun 2019 02:53:54: 16000000 INFO @ Mon, 03 Jun 2019 02:53:59: 16000000 INFO @ Mon, 03 Jun 2019 02:54:00: 15000000 INFO @ Mon, 03 Jun 2019 02:54:03: 17000000 INFO @ Mon, 03 Jun 2019 02:54:08: 17000000 INFO @ Mon, 03 Jun 2019 02:54:09: 16000000 INFO @ Mon, 03 Jun 2019 02:54:11: 18000000 INFO @ Mon, 03 Jun 2019 02:54:16: 18000000 INFO @ Mon, 03 Jun 2019 02:54:18: 17000000 INFO @ Mon, 03 Jun 2019 02:54:20: 19000000 INFO @ Mon, 03 Jun 2019 02:54:25: 19000000 INFO @ Mon, 03 Jun 2019 02:54:28: 18000000 INFO @ Mon, 03 Jun 2019 02:54:28: 20000000 INFO @ Mon, 03 Jun 2019 02:54:32: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:54:32: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:54:32: #1 total tags in treatment: 20416849 INFO @ Mon, 03 Jun 2019 02:54:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:54:32: #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 02:54:32: #1 tags after filtering in treatment: 20416849 INFO @ Mon, 03 Jun 2019 02:54:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:54:32: #1 finished! INFO @ Mon, 03 Jun 2019 02:54:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:54:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:54:34: 20000000 INFO @ Mon, 03 Jun 2019 02:54:34: #2 number of paired peaks: 2169 INFO @ Mon, 03 Jun 2019 02:54:34: start model_add_line... INFO @ Mon, 03 Jun 2019 02:54:34: start X-correlation... INFO @ Mon, 03 Jun 2019 02:54:34: end of X-cor INFO @ Mon, 03 Jun 2019 02:54:34: #2 finished! INFO @ Mon, 03 Jun 2019 02:54:34: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 02:54:34: #2 alternative fragment length(s) may be 1 bps INFO @ Mon, 03 Jun 2019 02:54:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.20_model.r WARNING @ Mon, 03 Jun 2019 02:54:34: #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, 03 Jun 2019 02:54:34: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Mon, 03 Jun 2019 02:54:34: #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 02:54:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:54:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:54:37: 19000000 INFO @ Mon, 03 Jun 2019 02:54:38: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:54:38: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:54:38: #1 total tags in treatment: 20416849 INFO @ Mon, 03 Jun 2019 02:54:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:54:38: #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 02:54:38: #1 tags after filtering in treatment: 20416849 INFO @ Mon, 03 Jun 2019 02:54:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:54:38: #1 finished! INFO @ Mon, 03 Jun 2019 02:54:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:54:40: #2 number of paired peaks: 2169 INFO @ Mon, 03 Jun 2019 02:54:40: start model_add_line... INFO @ Mon, 03 Jun 2019 02:54:40: start X-correlation... INFO @ Mon, 03 Jun 2019 02:54:40: end of X-cor INFO @ Mon, 03 Jun 2019 02:54:40: #2 finished! INFO @ Mon, 03 Jun 2019 02:54:40: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 02:54:40: #2 alternative fragment length(s) may be 1 bps INFO @ Mon, 03 Jun 2019 02:54:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.05_model.r WARNING @ Mon, 03 Jun 2019 02:54:40: #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, 03 Jun 2019 02:54:40: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Mon, 03 Jun 2019 02:54:40: #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 02:54:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:54:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:54:46: 20000000 INFO @ Mon, 03 Jun 2019 02:54:50: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 02:54:50: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 02:54:50: #1 total tags in treatment: 20416849 INFO @ Mon, 03 Jun 2019 02:54:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:54:50: #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 02:54:51: #1 tags after filtering in treatment: 20416849 INFO @ Mon, 03 Jun 2019 02:54:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:54:51: #1 finished! INFO @ Mon, 03 Jun 2019 02:54:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:54:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:54:53: #2 number of paired peaks: 2169 INFO @ Mon, 03 Jun 2019 02:54:53: start model_add_line... INFO @ Mon, 03 Jun 2019 02:54:53: start X-correlation... INFO @ Mon, 03 Jun 2019 02:54:53: end of X-cor INFO @ Mon, 03 Jun 2019 02:54:53: #2 finished! INFO @ Mon, 03 Jun 2019 02:54:53: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 02:54:53: #2 alternative fragment length(s) may be 1 bps INFO @ Mon, 03 Jun 2019 02:54:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.10_model.r WARNING @ Mon, 03 Jun 2019 02:54:53: #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, 03 Jun 2019 02:54:53: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Mon, 03 Jun 2019 02:54:53: #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 02:54:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:54:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:55:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:55:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:55:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:55:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:55:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:55:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.20_summits.bed INFO @ Mon, 03 Jun 2019 02:55:43: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:55:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:55:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:55:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.05_summits.bed INFO @ Mon, 03 Jun 2019 02:55:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:56:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:56:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:56:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX113332/SRX113332.10_summits.bed INFO @ Mon, 03 Jun 2019 02:56:03: Done! pass1 - making usageList (0 chroms): 0 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。