Job ID = 1293150 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 38,462,838 reads read : 38,462,838 reads written : 38,462,838 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:19 38462838 reads; of these: 38462838 (100.00%) were unpaired; of these: 7105851 (18.47%) aligned 0 times 27065655 (70.37%) aligned exactly 1 time 4291332 (11.16%) aligned >1 times 81.53% overall alignment rate Time searching: 00:08:20 Overall time: 00:08:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 6999451 / 31356987 = 0.2232 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 22:36:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.bam'] # control file = None # effective genome size = 9.00e+07 # 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 22:36:23: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:36:23: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:36:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.bam'] # control file = None # effective genome size = 9.00e+07 # 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 22:36:23: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:36:23: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:36:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.bam'] # control file = None # effective genome size = 9.00e+07 # 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 22:36:23: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:36:23: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:36:31: 1000000 INFO @ Sun, 02 Jun 2019 22:36:32: 1000000 INFO @ Sun, 02 Jun 2019 22:36:33: 1000000 INFO @ Sun, 02 Jun 2019 22:36:38: 2000000 INFO @ Sun, 02 Jun 2019 22:36:41: 2000000 INFO @ Sun, 02 Jun 2019 22:36:42: 2000000 INFO @ Sun, 02 Jun 2019 22:36:45: 3000000 INFO @ Sun, 02 Jun 2019 22:36:49: 3000000 INFO @ Sun, 02 Jun 2019 22:36:51: 3000000 INFO @ Sun, 02 Jun 2019 22:36:53: 4000000 INFO @ Sun, 02 Jun 2019 22:36:57: 4000000 INFO @ Sun, 02 Jun 2019 22:37:00: 5000000 INFO @ Sun, 02 Jun 2019 22:37:00: 4000000 INFO @ Sun, 02 Jun 2019 22:37:06: 5000000 INFO @ Sun, 02 Jun 2019 22:37:07: 6000000 INFO @ Sun, 02 Jun 2019 22:37:09: 5000000 INFO @ Sun, 02 Jun 2019 22:37:14: 6000000 INFO @ Sun, 02 Jun 2019 22:37:14: 7000000 INFO @ Sun, 02 Jun 2019 22:37:18: 6000000 INFO @ Sun, 02 Jun 2019 22:37:22: 8000000 INFO @ Sun, 02 Jun 2019 22:37:22: 7000000 INFO @ Sun, 02 Jun 2019 22:37:27: 7000000 INFO @ Sun, 02 Jun 2019 22:37:29: 9000000 INFO @ Sun, 02 Jun 2019 22:37:31: 8000000 INFO @ Sun, 02 Jun 2019 22:37:36: 10000000 INFO @ Sun, 02 Jun 2019 22:37:37: 8000000 INFO @ Sun, 02 Jun 2019 22:37:39: 9000000 INFO @ Sun, 02 Jun 2019 22:37:44: 11000000 INFO @ Sun, 02 Jun 2019 22:37:46: 9000000 INFO @ Sun, 02 Jun 2019 22:37:47: 10000000 INFO @ Sun, 02 Jun 2019 22:37:51: 12000000 INFO @ Sun, 02 Jun 2019 22:37:55: 10000000 INFO @ Sun, 02 Jun 2019 22:37:56: 11000000 INFO @ Sun, 02 Jun 2019 22:37:58: 13000000 INFO @ Sun, 02 Jun 2019 22:38:04: 11000000 INFO @ Sun, 02 Jun 2019 22:38:04: 12000000 INFO @ Sun, 02 Jun 2019 22:38:06: 14000000 INFO @ Sun, 02 Jun 2019 22:38:12: 13000000 INFO @ Sun, 02 Jun 2019 22:38:13: 15000000 INFO @ Sun, 02 Jun 2019 22:38:13: 12000000 INFO @ Sun, 02 Jun 2019 22:38:20: 16000000 INFO @ Sun, 02 Jun 2019 22:38:20: 14000000 INFO @ Sun, 02 Jun 2019 22:38:23: 13000000 INFO @ Sun, 02 Jun 2019 22:38:27: 17000000 INFO @ Sun, 02 Jun 2019 22:38:28: 15000000 INFO @ Sun, 02 Jun 2019 22:38:32: 14000000 INFO @ Sun, 02 Jun 2019 22:38:34: 18000000 INFO @ Sun, 02 Jun 2019 22:38:36: 16000000 INFO @ Sun, 02 Jun 2019 22:38:41: 15000000 INFO @ Sun, 02 Jun 2019 22:38:41: 19000000 INFO @ Sun, 02 Jun 2019 22:38:44: 17000000 INFO @ Sun, 02 Jun 2019 22:38:49: 20000000 INFO @ Sun, 02 Jun 2019 22:38:50: 16000000 INFO @ Sun, 02 Jun 2019 22:38:52: 18000000 INFO @ Sun, 02 Jun 2019 22:38:56: 21000000 INFO @ Sun, 02 Jun 2019 22:38:59: 17000000 INFO @ Sun, 02 Jun 2019 22:39:00: 19000000 INFO @ Sun, 02 Jun 2019 22:39:03: 22000000 INFO @ Sun, 02 Jun 2019 22:39:08: 18000000 INFO @ Sun, 02 Jun 2019 22:39:08: 20000000 INFO @ Sun, 02 Jun 2019 22:39:11: 23000000 INFO @ Sun, 02 Jun 2019 22:39:16: 21000000 INFO @ Sun, 02 Jun 2019 22:39:17: 19000000 INFO @ Sun, 02 Jun 2019 22:39:20: 24000000 INFO @ Sun, 02 Jun 2019 22:39:23: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:39:23: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:39:23: #1 total tags in treatment: 24357536 INFO @ Sun, 02 Jun 2019 22:39:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:39:23: #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 22:39:24: #1 tags after filtering in treatment: 24357536 INFO @ Sun, 02 Jun 2019 22:39:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:39:24: #1 finished! INFO @ Sun, 02 Jun 2019 22:39:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:39:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:39:24: 22000000 INFO @ Sun, 02 Jun 2019 22:39:26: 20000000 INFO @ Sun, 02 Jun 2019 22:39:26: #2 number of paired peaks: 132 WARNING @ Sun, 02 Jun 2019 22:39:26: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sun, 02 Jun 2019 22:39:26: start model_add_line... INFO @ Sun, 02 Jun 2019 22:39:26: start X-correlation... INFO @ Sun, 02 Jun 2019 22:39:26: end of X-cor INFO @ Sun, 02 Jun 2019 22:39:26: #2 finished! INFO @ Sun, 02 Jun 2019 22:39:26: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:39:26: #2 alternative fragment length(s) may be 1,12,44,479,585 bps INFO @ Sun, 02 Jun 2019 22:39:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.05_model.r WARNING @ Sun, 02 Jun 2019 22:39:26: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:39:26: #2 You may need to consider one of the other alternative d(s): 1,12,44,479,585 WARNING @ Sun, 02 Jun 2019 22:39:26: #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 22:39:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:39:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:39:33: 23000000 INFO @ Sun, 02 Jun 2019 22:39:34: 21000000 INFO @ Sun, 02 Jun 2019 22:39:41: 24000000 INFO @ Sun, 02 Jun 2019 22:39:43: 22000000 INFO @ Sun, 02 Jun 2019 22:39:44: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:39:44: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:39:44: #1 total tags in treatment: 24357536 INFO @ Sun, 02 Jun 2019 22:39:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:39:44: #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 22:39:45: #1 tags after filtering in treatment: 24357536 INFO @ Sun, 02 Jun 2019 22:39:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:39:45: #1 finished! INFO @ Sun, 02 Jun 2019 22:39:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:39:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:39:47: #2 number of paired peaks: 132 WARNING @ Sun, 02 Jun 2019 22:39:47: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sun, 02 Jun 2019 22:39:47: start model_add_line... INFO @ Sun, 02 Jun 2019 22:39:47: start X-correlation... INFO @ Sun, 02 Jun 2019 22:39:47: end of X-cor INFO @ Sun, 02 Jun 2019 22:39:47: #2 finished! INFO @ Sun, 02 Jun 2019 22:39:47: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:39:47: #2 alternative fragment length(s) may be 1,12,44,479,585 bps INFO @ Sun, 02 Jun 2019 22:39:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.10_model.r WARNING @ Sun, 02 Jun 2019 22:39:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:39:47: #2 You may need to consider one of the other alternative d(s): 1,12,44,479,585 WARNING @ Sun, 02 Jun 2019 22:39:47: #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 22:39:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:39:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:39:52: 23000000 INFO @ Sun, 02 Jun 2019 22:40:01: 24000000 INFO @ Sun, 02 Jun 2019 22:40:04: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:40:04: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:40:04: #1 total tags in treatment: 24357536 INFO @ Sun, 02 Jun 2019 22:40:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:40:04: #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 22:40:04: #1 tags after filtering in treatment: 24357536 INFO @ Sun, 02 Jun 2019 22:40:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:40:04: #1 finished! INFO @ Sun, 02 Jun 2019 22:40:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:40:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:40:06: #2 number of paired peaks: 132 WARNING @ Sun, 02 Jun 2019 22:40:06: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sun, 02 Jun 2019 22:40:06: start model_add_line... INFO @ Sun, 02 Jun 2019 22:40:07: start X-correlation... INFO @ Sun, 02 Jun 2019 22:40:07: end of X-cor INFO @ Sun, 02 Jun 2019 22:40:07: #2 finished! INFO @ Sun, 02 Jun 2019 22:40:07: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:40:07: #2 alternative fragment length(s) may be 1,12,44,479,585 bps INFO @ Sun, 02 Jun 2019 22:40:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.20_model.r WARNING @ Sun, 02 Jun 2019 22:40:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:40:07: #2 You may need to consider one of the other alternative d(s): 1,12,44,479,585 WARNING @ Sun, 02 Jun 2019 22:40:07: #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 22:40:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:40:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:40:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:40:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:40:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:40:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:40:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.05_summits.bed INFO @ Sun, 02 Jun 2019 22:40:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:40:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.10_summits.bed INFO @ Sun, 02 Jun 2019 22:40:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:41:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:41:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:41:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402718/SRX5402718.20_summits.bed INFO @ Sun, 02 Jun 2019 22:41:16: 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。