Job ID = 1292020 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,453,149 reads read : 58,906,298 reads written : 29,453,149 reads 0-length : 29,453,149 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: 00:09:28 29453149 reads; of these: 29453149 (100.00%) were unpaired; of these: 613393 (2.08%) aligned 0 times 24066240 (81.71%) aligned exactly 1 time 4773516 (16.21%) aligned >1 times 97.92% overall alignment rate Time searching: 00:09:28 Overall time: 00:09:28 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 12 files... [bam_rmdupse_core] 3394287 / 28839756 = 0.1177 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 17:33:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.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 17:33:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:33:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:33:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.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 17:33:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:33:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:33:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.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 17:33:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:33:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:33:23: 1000000 INFO @ Sun, 02 Jun 2019 17:33:23: 1000000 INFO @ Sun, 02 Jun 2019 17:33:23: 1000000 INFO @ Sun, 02 Jun 2019 17:33:32: 2000000 INFO @ Sun, 02 Jun 2019 17:33:32: 2000000 INFO @ Sun, 02 Jun 2019 17:33:33: 2000000 INFO @ Sun, 02 Jun 2019 17:33:40: 3000000 INFO @ Sun, 02 Jun 2019 17:33:41: 3000000 INFO @ Sun, 02 Jun 2019 17:33:43: 3000000 INFO @ Sun, 02 Jun 2019 17:33:49: 4000000 INFO @ Sun, 02 Jun 2019 17:33:50: 4000000 INFO @ Sun, 02 Jun 2019 17:33:53: 4000000 INFO @ Sun, 02 Jun 2019 17:33:58: 5000000 INFO @ Sun, 02 Jun 2019 17:33:59: 5000000 INFO @ Sun, 02 Jun 2019 17:34:03: 5000000 INFO @ Sun, 02 Jun 2019 17:34:07: 6000000 INFO @ Sun, 02 Jun 2019 17:34:08: 6000000 INFO @ Sun, 02 Jun 2019 17:34:12: 6000000 INFO @ Sun, 02 Jun 2019 17:34:16: 7000000 INFO @ Sun, 02 Jun 2019 17:34:17: 7000000 INFO @ Sun, 02 Jun 2019 17:34:22: 7000000 INFO @ Sun, 02 Jun 2019 17:34:24: 8000000 INFO @ Sun, 02 Jun 2019 17:34:26: 8000000 INFO @ Sun, 02 Jun 2019 17:34:32: 8000000 INFO @ Sun, 02 Jun 2019 17:34:33: 9000000 INFO @ Sun, 02 Jun 2019 17:34:35: 9000000 INFO @ Sun, 02 Jun 2019 17:34:41: 10000000 INFO @ Sun, 02 Jun 2019 17:34:43: 9000000 INFO @ Sun, 02 Jun 2019 17:34:45: 10000000 INFO @ Sun, 02 Jun 2019 17:34:50: 11000000 INFO @ Sun, 02 Jun 2019 17:34:53: 11000000 INFO @ Sun, 02 Jun 2019 17:34:54: 10000000 INFO @ Sun, 02 Jun 2019 17:34:59: 12000000 INFO @ Sun, 02 Jun 2019 17:35:02: 12000000 INFO @ Sun, 02 Jun 2019 17:35:04: 11000000 INFO @ Sun, 02 Jun 2019 17:35:08: 13000000 INFO @ Sun, 02 Jun 2019 17:35:11: 13000000 INFO @ Sun, 02 Jun 2019 17:35:15: 12000000 INFO @ Sun, 02 Jun 2019 17:35:17: 14000000 INFO @ Sun, 02 Jun 2019 17:35:20: 14000000 INFO @ Sun, 02 Jun 2019 17:35:25: 13000000 INFO @ Sun, 02 Jun 2019 17:35:26: 15000000 INFO @ Sun, 02 Jun 2019 17:35:29: 15000000 INFO @ Sun, 02 Jun 2019 17:35:34: 16000000 INFO @ Sun, 02 Jun 2019 17:35:36: 14000000 INFO @ Sun, 02 Jun 2019 17:35:38: 16000000 INFO @ Sun, 02 Jun 2019 17:35:46: 17000000 INFO @ Sun, 02 Jun 2019 17:35:47: 17000000 INFO @ Sun, 02 Jun 2019 17:35:48: 15000000 INFO @ Sun, 02 Jun 2019 17:35:55: 18000000 INFO @ Sun, 02 Jun 2019 17:35:56: 18000000 INFO @ Sun, 02 Jun 2019 17:35:58: 16000000 INFO @ Sun, 02 Jun 2019 17:36:03: 19000000 INFO @ Sun, 02 Jun 2019 17:36:05: 19000000 INFO @ Sun, 02 Jun 2019 17:36:09: 17000000 INFO @ Sun, 02 Jun 2019 17:36:12: 20000000 INFO @ Sun, 02 Jun 2019 17:36:14: 20000000 INFO @ Sun, 02 Jun 2019 17:36:19: 18000000 INFO @ Sun, 02 Jun 2019 17:36:21: 21000000 INFO @ Sun, 02 Jun 2019 17:36:23: 21000000 INFO @ Sun, 02 Jun 2019 17:36:29: 22000000 INFO @ Sun, 02 Jun 2019 17:36:30: 19000000 INFO @ Sun, 02 Jun 2019 17:36:32: 22000000 INFO @ Sun, 02 Jun 2019 17:36:38: 23000000 INFO @ Sun, 02 Jun 2019 17:36:40: 20000000 INFO @ Sun, 02 Jun 2019 17:36:41: 23000000 INFO @ Sun, 02 Jun 2019 17:36:46: 24000000 INFO @ Sun, 02 Jun 2019 17:36:50: 24000000 INFO @ Sun, 02 Jun 2019 17:36:51: 21000000 INFO @ Sun, 02 Jun 2019 17:36:54: 25000000 INFO @ Sun, 02 Jun 2019 17:36:58: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:36:58: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:36:58: #1 total tags in treatment: 25445469 INFO @ Sun, 02 Jun 2019 17:36:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:36:58: #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 17:36:59: #1 tags after filtering in treatment: 25445469 INFO @ Sun, 02 Jun 2019 17:36:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:36:59: #1 finished! INFO @ Sun, 02 Jun 2019 17:36:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:36:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:36:59: 25000000 INFO @ Sun, 02 Jun 2019 17:37:01: 22000000 INFO @ Sun, 02 Jun 2019 17:37:01: #2 number of paired peaks: 120 WARNING @ Sun, 02 Jun 2019 17:37:01: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Sun, 02 Jun 2019 17:37:01: start model_add_line... INFO @ Sun, 02 Jun 2019 17:37:02: start X-correlation... INFO @ Sun, 02 Jun 2019 17:37:02: end of X-cor INFO @ Sun, 02 Jun 2019 17:37:02: #2 finished! INFO @ Sun, 02 Jun 2019 17:37:02: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 17:37:02: #2 alternative fragment length(s) may be 1,42,477,518,566 bps INFO @ Sun, 02 Jun 2019 17:37:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.20_model.r WARNING @ Sun, 02 Jun 2019 17:37:02: #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 17:37:02: #2 You may need to consider one of the other alternative d(s): 1,42,477,518,566 WARNING @ Sun, 02 Jun 2019 17:37:02: #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 17:37:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:37:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:37:03: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:37:03: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:37:03: #1 total tags in treatment: 25445469 INFO @ Sun, 02 Jun 2019 17:37:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:37:03: #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 17:37:04: #1 tags after filtering in treatment: 25445469 INFO @ Sun, 02 Jun 2019 17:37:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:37:04: #1 finished! INFO @ Sun, 02 Jun 2019 17:37:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:37:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:37:06: #2 number of paired peaks: 120 WARNING @ Sun, 02 Jun 2019 17:37:06: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Sun, 02 Jun 2019 17:37:06: start model_add_line... INFO @ Sun, 02 Jun 2019 17:37:06: start X-correlation... INFO @ Sun, 02 Jun 2019 17:37:06: end of X-cor INFO @ Sun, 02 Jun 2019 17:37:06: #2 finished! INFO @ Sun, 02 Jun 2019 17:37:06: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 17:37:06: #2 alternative fragment length(s) may be 1,42,477,518,566 bps INFO @ Sun, 02 Jun 2019 17:37:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.10_model.r WARNING @ Sun, 02 Jun 2019 17:37:06: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:37:06: #2 You may need to consider one of the other alternative d(s): 1,42,477,518,566 WARNING @ Sun, 02 Jun 2019 17:37:06: #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 17:37:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:37:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:37:12: 23000000 INFO @ Sun, 02 Jun 2019 17:37:22: 24000000 INFO @ Sun, 02 Jun 2019 17:37:32: 25000000 INFO @ Sun, 02 Jun 2019 17:37:37: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:37:37: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:37:37: #1 total tags in treatment: 25445469 INFO @ Sun, 02 Jun 2019 17:37:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:37:37: #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 17:37:37: #1 tags after filtering in treatment: 25445469 INFO @ Sun, 02 Jun 2019 17:37:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:37:37: #1 finished! INFO @ Sun, 02 Jun 2019 17:37:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:37:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:37:40: #2 number of paired peaks: 120 WARNING @ Sun, 02 Jun 2019 17:37:40: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Sun, 02 Jun 2019 17:37:40: start model_add_line... INFO @ Sun, 02 Jun 2019 17:37:40: start X-correlation... INFO @ Sun, 02 Jun 2019 17:37:40: end of X-cor INFO @ Sun, 02 Jun 2019 17:37:40: #2 finished! INFO @ Sun, 02 Jun 2019 17:37:40: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 17:37:40: #2 alternative fragment length(s) may be 1,42,477,518,566 bps INFO @ Sun, 02 Jun 2019 17:37:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.05_model.r WARNING @ Sun, 02 Jun 2019 17:37:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:37:40: #2 You may need to consider one of the other alternative d(s): 1,42,477,518,566 WARNING @ Sun, 02 Jun 2019 17:37:40: #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 17:37:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:37:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:37:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:38:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:38:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:38:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:38:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.20_summits.bed INFO @ Sun, 02 Jun 2019 17:38:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:38:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:38:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:38:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.10_summits.bed INFO @ Sun, 02 Jun 2019 17:38:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:38:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:39:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:39:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:39:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3104610/SRX3104610.05_summits.bed INFO @ Sun, 02 Jun 2019 17:39:05: 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。