Job ID = 1291525 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,808,649 reads read : 23,808,649 reads written : 23,808,649 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: 00:06:29 23808649 reads; of these: 23808649 (100.00%) were unpaired; of these: 651861 (2.74%) aligned 0 times 17196819 (72.23%) aligned exactly 1 time 5959969 (25.03%) aligned >1 times 97.26% overall alignment rate Time searching: 00:06:29 Overall time: 00:06:29 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 8 files... [bam_rmdupse_core] 9908097 / 23156788 = 0.4279 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 16:12:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.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 16:12:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:12:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:12:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.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 16:12:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:12:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:12:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.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 16:12:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:12:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:13:01: 1000000 INFO @ Sun, 02 Jun 2019 16:13:02: 1000000 INFO @ Sun, 02 Jun 2019 16:13:03: 1000000 INFO @ Sun, 02 Jun 2019 16:13:09: 2000000 INFO @ Sun, 02 Jun 2019 16:13:12: 2000000 INFO @ Sun, 02 Jun 2019 16:13:12: 2000000 INFO @ Sun, 02 Jun 2019 16:13:17: 3000000 INFO @ Sun, 02 Jun 2019 16:13:21: 3000000 INFO @ Sun, 02 Jun 2019 16:13:22: 3000000 INFO @ Sun, 02 Jun 2019 16:13:25: 4000000 INFO @ Sun, 02 Jun 2019 16:13:30: 4000000 INFO @ Sun, 02 Jun 2019 16:13:31: 4000000 INFO @ Sun, 02 Jun 2019 16:13:33: 5000000 INFO @ Sun, 02 Jun 2019 16:13:38: 5000000 INFO @ Sun, 02 Jun 2019 16:13:40: 5000000 INFO @ Sun, 02 Jun 2019 16:13:41: 6000000 INFO @ Sun, 02 Jun 2019 16:13:47: 6000000 INFO @ Sun, 02 Jun 2019 16:13:49: 7000000 INFO @ Sun, 02 Jun 2019 16:13:49: 6000000 INFO @ Sun, 02 Jun 2019 16:13:56: 7000000 INFO @ Sun, 02 Jun 2019 16:13:57: 8000000 INFO @ Sun, 02 Jun 2019 16:13:59: 7000000 INFO @ Sun, 02 Jun 2019 16:14:05: 9000000 INFO @ Sun, 02 Jun 2019 16:14:05: 8000000 INFO @ Sun, 02 Jun 2019 16:14:08: 8000000 INFO @ Sun, 02 Jun 2019 16:14:13: 10000000 INFO @ Sun, 02 Jun 2019 16:14:14: 9000000 INFO @ Sun, 02 Jun 2019 16:14:17: 9000000 INFO @ Sun, 02 Jun 2019 16:14:21: 11000000 INFO @ Sun, 02 Jun 2019 16:14:23: 10000000 INFO @ Sun, 02 Jun 2019 16:14:26: 10000000 INFO @ Sun, 02 Jun 2019 16:14:29: 12000000 INFO @ Sun, 02 Jun 2019 16:14:32: 11000000 INFO @ Sun, 02 Jun 2019 16:14:35: 11000000 INFO @ Sun, 02 Jun 2019 16:14:37: 13000000 INFO @ Sun, 02 Jun 2019 16:14:39: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:14:39: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:14:39: #1 total tags in treatment: 13248691 INFO @ Sun, 02 Jun 2019 16:14:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:14:39: #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 16:14:39: #1 tags after filtering in treatment: 13248691 INFO @ Sun, 02 Jun 2019 16:14:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:14:39: #1 finished! INFO @ Sun, 02 Jun 2019 16:14:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:14:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:14:40: #2 number of paired peaks: 169 WARNING @ Sun, 02 Jun 2019 16:14:40: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sun, 02 Jun 2019 16:14:40: start model_add_line... INFO @ Sun, 02 Jun 2019 16:14:40: start X-correlation... INFO @ Sun, 02 Jun 2019 16:14:40: end of X-cor INFO @ Sun, 02 Jun 2019 16:14:40: #2 finished! INFO @ Sun, 02 Jun 2019 16:14:40: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:14:40: #2 alternative fragment length(s) may be 1,38,91,117,143,171,216,266,401,423,482,506,541,546,555,583 bps INFO @ Sun, 02 Jun 2019 16:14:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.05_model.r WARNING @ Sun, 02 Jun 2019 16:14:40: #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 16:14:40: #2 You may need to consider one of the other alternative d(s): 1,38,91,117,143,171,216,266,401,423,482,506,541,546,555,583 WARNING @ Sun, 02 Jun 2019 16:14:40: #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 16:14:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:14:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:14:40: 12000000 INFO @ Sun, 02 Jun 2019 16:14:44: 12000000 INFO @ Sun, 02 Jun 2019 16:14:49: 13000000 INFO @ Sun, 02 Jun 2019 16:14:51: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:14:51: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:14:51: #1 total tags in treatment: 13248691 INFO @ Sun, 02 Jun 2019 16:14:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:14:51: #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 16:14:52: #1 tags after filtering in treatment: 13248691 INFO @ Sun, 02 Jun 2019 16:14:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:14:52: #1 finished! INFO @ Sun, 02 Jun 2019 16:14:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:14:53: #2 number of paired peaks: 169 WARNING @ Sun, 02 Jun 2019 16:14:53: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sun, 02 Jun 2019 16:14:53: start model_add_line... INFO @ Sun, 02 Jun 2019 16:14:53: start X-correlation... INFO @ Sun, 02 Jun 2019 16:14:53: end of X-cor INFO @ Sun, 02 Jun 2019 16:14:53: #2 finished! INFO @ Sun, 02 Jun 2019 16:14:53: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:14:53: #2 alternative fragment length(s) may be 1,38,91,117,143,171,216,266,401,423,482,506,541,546,555,583 bps INFO @ Sun, 02 Jun 2019 16:14:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.10_model.r WARNING @ Sun, 02 Jun 2019 16:14:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:14:53: #2 You may need to consider one of the other alternative d(s): 1,38,91,117,143,171,216,266,401,423,482,506,541,546,555,583 WARNING @ Sun, 02 Jun 2019 16:14:53: #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 16:14:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:14:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:14:53: 13000000 INFO @ Sun, 02 Jun 2019 16:14:56: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:14:56: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:14:56: #1 total tags in treatment: 13248691 INFO @ Sun, 02 Jun 2019 16:14:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:14:56: #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 16:14:56: #1 tags after filtering in treatment: 13248691 INFO @ Sun, 02 Jun 2019 16:14:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:14:56: #1 finished! INFO @ Sun, 02 Jun 2019 16:14:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:14:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:14:57: #2 number of paired peaks: 169 WARNING @ Sun, 02 Jun 2019 16:14:57: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sun, 02 Jun 2019 16:14:57: start model_add_line... INFO @ Sun, 02 Jun 2019 16:14:57: start X-correlation... INFO @ Sun, 02 Jun 2019 16:14:57: end of X-cor INFO @ Sun, 02 Jun 2019 16:14:57: #2 finished! INFO @ Sun, 02 Jun 2019 16:14:57: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 16:14:57: #2 alternative fragment length(s) may be 1,38,91,117,143,171,216,266,401,423,482,506,541,546,555,583 bps INFO @ Sun, 02 Jun 2019 16:14:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.20_model.r WARNING @ Sun, 02 Jun 2019 16:14:57: #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 16:14:57: #2 You may need to consider one of the other alternative d(s): 1,38,91,117,143,171,216,266,401,423,482,506,541,546,555,583 WARNING @ Sun, 02 Jun 2019 16:14:57: #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 16:14:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:14:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:15:10: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:15:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:15:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:15:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:15:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.05_summits.bed INFO @ Sun, 02 Jun 2019 16:15:23: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:15:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:15:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:15:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:15:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.10_summits.bed INFO @ Sun, 02 Jun 2019 16:15:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:15:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:15:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:15:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113603/SRX113603.20_summits.bed INFO @ Sun, 02 Jun 2019 16:15:40: 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。