Job ID = 1293124 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,481,793 reads read : 27,481,793 reads written : 27,481,793 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: 00:06:30 27481793 reads; of these: 27481793 (100.00%) were unpaired; of these: 5497756 (20.01%) aligned 0 times 16133974 (58.71%) aligned exactly 1 time 5850063 (21.29%) aligned >1 times 79.99% overall alignment rate Time searching: 00:06:30 Overall time: 00:06:30 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] 9162587 / 21984037 = 0.4168 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 22:15:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.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 22:15:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:15:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:15:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.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 22:15:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:15:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:15:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.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 22:15:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:15:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:15:43: 1000000 INFO @ Sun, 02 Jun 2019 22:15:44: 1000000 INFO @ Sun, 02 Jun 2019 22:15:45: 1000000 INFO @ Sun, 02 Jun 2019 22:15:50: 2000000 INFO @ Sun, 02 Jun 2019 22:15:52: 2000000 INFO @ Sun, 02 Jun 2019 22:15:55: 2000000 INFO @ Sun, 02 Jun 2019 22:15:58: 3000000 INFO @ Sun, 02 Jun 2019 22:16:00: 3000000 INFO @ Sun, 02 Jun 2019 22:16:04: 3000000 INFO @ Sun, 02 Jun 2019 22:16:06: 4000000 INFO @ Sun, 02 Jun 2019 22:16:09: 4000000 INFO @ Sun, 02 Jun 2019 22:16:14: 5000000 INFO @ Sun, 02 Jun 2019 22:16:14: 4000000 INFO @ Sun, 02 Jun 2019 22:16:18: 5000000 INFO @ Sun, 02 Jun 2019 22:16:21: 6000000 INFO @ Sun, 02 Jun 2019 22:16:24: 5000000 INFO @ Sun, 02 Jun 2019 22:16:26: 6000000 INFO @ Sun, 02 Jun 2019 22:16:29: 7000000 INFO @ Sun, 02 Jun 2019 22:16:34: 6000000 INFO @ Sun, 02 Jun 2019 22:16:35: 7000000 INFO @ Sun, 02 Jun 2019 22:16:36: 8000000 INFO @ Sun, 02 Jun 2019 22:16:43: 8000000 INFO @ Sun, 02 Jun 2019 22:16:44: 7000000 INFO @ Sun, 02 Jun 2019 22:16:44: 9000000 INFO @ Sun, 02 Jun 2019 22:16:51: 10000000 INFO @ Sun, 02 Jun 2019 22:16:51: 9000000 INFO @ Sun, 02 Jun 2019 22:16:53: 8000000 INFO @ Sun, 02 Jun 2019 22:16:59: 11000000 INFO @ Sun, 02 Jun 2019 22:17:00: 10000000 INFO @ Sun, 02 Jun 2019 22:17:03: 9000000 INFO @ Sun, 02 Jun 2019 22:17:06: 12000000 INFO @ Sun, 02 Jun 2019 22:17:08: 11000000 INFO @ Sun, 02 Jun 2019 22:17:12: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:17:12: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:17:12: #1 total tags in treatment: 12821450 INFO @ Sun, 02 Jun 2019 22:17:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:17:12: #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 22:17:12: 10000000 INFO @ Sun, 02 Jun 2019 22:17:13: #1 tags after filtering in treatment: 12821450 INFO @ Sun, 02 Jun 2019 22:17:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:17:13: #1 finished! INFO @ Sun, 02 Jun 2019 22:17:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:17:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:17:14: #2 number of paired peaks: 625 WARNING @ Sun, 02 Jun 2019 22:17:14: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Sun, 02 Jun 2019 22:17:14: start model_add_line... INFO @ Sun, 02 Jun 2019 22:17:14: start X-correlation... INFO @ Sun, 02 Jun 2019 22:17:14: end of X-cor INFO @ Sun, 02 Jun 2019 22:17:14: #2 finished! INFO @ Sun, 02 Jun 2019 22:17:14: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:17:14: #2 alternative fragment length(s) may be 1,42,557 bps INFO @ Sun, 02 Jun 2019 22:17:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.10_model.r WARNING @ Sun, 02 Jun 2019 22:17:14: #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 22:17:14: #2 You may need to consider one of the other alternative d(s): 1,42,557 WARNING @ Sun, 02 Jun 2019 22:17:14: #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 22:17:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:17:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:17:16: 12000000 INFO @ Sun, 02 Jun 2019 22:17:22: 11000000 INFO @ Sun, 02 Jun 2019 22:17:23: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:17:23: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:17:23: #1 total tags in treatment: 12821450 INFO @ Sun, 02 Jun 2019 22:17:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:17:23: #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 22:17:23: #1 tags after filtering in treatment: 12821450 INFO @ Sun, 02 Jun 2019 22:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:17:23: #1 finished! INFO @ Sun, 02 Jun 2019 22:17:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:17:24: #2 number of paired peaks: 625 WARNING @ Sun, 02 Jun 2019 22:17:24: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Sun, 02 Jun 2019 22:17:24: start model_add_line... INFO @ Sun, 02 Jun 2019 22:17:24: start X-correlation... INFO @ Sun, 02 Jun 2019 22:17:24: end of X-cor INFO @ Sun, 02 Jun 2019 22:17:24: #2 finished! INFO @ Sun, 02 Jun 2019 22:17:24: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:17:24: #2 alternative fragment length(s) may be 1,42,557 bps INFO @ Sun, 02 Jun 2019 22:17:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.05_model.r WARNING @ Sun, 02 Jun 2019 22:17:24: #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 22:17:24: #2 You may need to consider one of the other alternative d(s): 1,42,557 WARNING @ Sun, 02 Jun 2019 22:17:24: #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 22:17:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:17:32: 12000000 INFO @ Sun, 02 Jun 2019 22:17:39: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:17:39: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:17:39: #1 total tags in treatment: 12821450 INFO @ Sun, 02 Jun 2019 22:17:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:17:39: #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 22:17:39: #1 tags after filtering in treatment: 12821450 INFO @ Sun, 02 Jun 2019 22:17:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:17:39: #1 finished! INFO @ Sun, 02 Jun 2019 22:17:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:17:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:17:40: #2 number of paired peaks: 625 WARNING @ Sun, 02 Jun 2019 22:17:40: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Sun, 02 Jun 2019 22:17:40: start model_add_line... INFO @ Sun, 02 Jun 2019 22:17:40: start X-correlation... INFO @ Sun, 02 Jun 2019 22:17:41: end of X-cor INFO @ Sun, 02 Jun 2019 22:17:41: #2 finished! INFO @ Sun, 02 Jun 2019 22:17:41: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:17:41: #2 alternative fragment length(s) may be 1,42,557 bps INFO @ Sun, 02 Jun 2019 22:17:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.20_model.r WARNING @ Sun, 02 Jun 2019 22:17:41: #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 22:17:41: #2 You may need to consider one of the other alternative d(s): 1,42,557 WARNING @ Sun, 02 Jun 2019 22:17:41: #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 22:17:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:17:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:17:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:17:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:17:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:17:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.10_summits.bed INFO @ Sun, 02 Jun 2019 22:17:59: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:18:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:18:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:18:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.05_summits.bed INFO @ Sun, 02 Jun 2019 22:18:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:18:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:18:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:18:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:18:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402700/SRX5402700.20_summits.bed INFO @ Sun, 02 Jun 2019 22:18:26: 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。