Job ID = 1293218 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,340,592 reads read : 36,340,592 reads written : 36,340,592 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: 00:06:22 36340592 reads; of these: 36340592 (100.00%) were unpaired; of these: 16638551 (45.79%) aligned 0 times 16273121 (44.78%) aligned exactly 1 time 3428920 (9.44%) aligned >1 times 54.21% overall alignment rate Time searching: 00:06:22 Overall time: 00:06:22 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] 2181604 / 19702041 = 0.1107 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 22:50:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.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 22:50:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:50:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:50:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.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 22:50:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:50:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:50:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.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 22:50:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:50:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:50:20: 1000000 INFO @ Sun, 02 Jun 2019 22:50:23: 1000000 INFO @ Sun, 02 Jun 2019 22:50:23: 1000000 INFO @ Sun, 02 Jun 2019 22:50:27: 2000000 INFO @ Sun, 02 Jun 2019 22:50:30: 2000000 INFO @ Sun, 02 Jun 2019 22:50:32: 2000000 INFO @ Sun, 02 Jun 2019 22:50:33: 3000000 INFO @ Sun, 02 Jun 2019 22:50:38: 3000000 INFO @ Sun, 02 Jun 2019 22:50:40: 4000000 INFO @ Sun, 02 Jun 2019 22:50:40: 3000000 INFO @ Sun, 02 Jun 2019 22:50:46: 4000000 INFO @ Sun, 02 Jun 2019 22:50:47: 5000000 INFO @ Sun, 02 Jun 2019 22:50:49: 4000000 INFO @ Sun, 02 Jun 2019 22:50:54: 5000000 INFO @ Sun, 02 Jun 2019 22:50:54: 6000000 INFO @ Sun, 02 Jun 2019 22:50:57: 5000000 INFO @ Sun, 02 Jun 2019 22:51:02: 7000000 INFO @ Sun, 02 Jun 2019 22:51:02: 6000000 INFO @ Sun, 02 Jun 2019 22:51:05: 6000000 INFO @ Sun, 02 Jun 2019 22:51:09: 8000000 INFO @ Sun, 02 Jun 2019 22:51:10: 7000000 INFO @ Sun, 02 Jun 2019 22:51:13: 7000000 INFO @ Sun, 02 Jun 2019 22:51:17: 9000000 INFO @ Sun, 02 Jun 2019 22:51:18: 8000000 INFO @ Sun, 02 Jun 2019 22:51:20: 8000000 INFO @ Sun, 02 Jun 2019 22:51:24: 10000000 INFO @ Sun, 02 Jun 2019 22:51:25: 9000000 INFO @ Sun, 02 Jun 2019 22:51:28: 9000000 INFO @ Sun, 02 Jun 2019 22:51:32: 11000000 INFO @ Sun, 02 Jun 2019 22:51:33: 10000000 INFO @ Sun, 02 Jun 2019 22:51:35: 10000000 INFO @ Sun, 02 Jun 2019 22:51:40: 12000000 INFO @ Sun, 02 Jun 2019 22:51:40: 11000000 INFO @ Sun, 02 Jun 2019 22:51:43: 11000000 INFO @ Sun, 02 Jun 2019 22:51:47: 13000000 INFO @ Sun, 02 Jun 2019 22:51:48: 12000000 INFO @ Sun, 02 Jun 2019 22:51:51: 12000000 INFO @ Sun, 02 Jun 2019 22:51:54: 14000000 INFO @ Sun, 02 Jun 2019 22:51:56: 13000000 INFO @ Sun, 02 Jun 2019 22:51:58: 13000000 INFO @ Sun, 02 Jun 2019 22:52:02: 15000000 INFO @ Sun, 02 Jun 2019 22:52:03: 14000000 INFO @ Sun, 02 Jun 2019 22:52:05: 14000000 INFO @ Sun, 02 Jun 2019 22:52:09: 16000000 INFO @ Sun, 02 Jun 2019 22:52:11: 15000000 INFO @ Sun, 02 Jun 2019 22:52:13: 15000000 INFO @ Sun, 02 Jun 2019 22:52:17: 17000000 INFO @ Sun, 02 Jun 2019 22:52:18: 16000000 INFO @ Sun, 02 Jun 2019 22:52:20: 16000000 INFO @ Sun, 02 Jun 2019 22:52:21: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:52:21: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:52:21: #1 total tags in treatment: 17520437 INFO @ Sun, 02 Jun 2019 22:52:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:52:21: #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 22:52:21: #1 tags after filtering in treatment: 17520437 INFO @ Sun, 02 Jun 2019 22:52:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:52:21: #1 finished! INFO @ Sun, 02 Jun 2019 22:52:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:52:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:52:23: #2 number of paired peaks: 239 WARNING @ Sun, 02 Jun 2019 22:52:23: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Sun, 02 Jun 2019 22:52:23: start model_add_line... INFO @ Sun, 02 Jun 2019 22:52:23: start X-correlation... INFO @ Sun, 02 Jun 2019 22:52:23: end of X-cor INFO @ Sun, 02 Jun 2019 22:52:23: #2 finished! INFO @ Sun, 02 Jun 2019 22:52:23: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:52:23: #2 alternative fragment length(s) may be 1,42,562 bps INFO @ Sun, 02 Jun 2019 22:52:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.05_model.r WARNING @ Sun, 02 Jun 2019 22:52:23: #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 22:52:23: #2 You may need to consider one of the other alternative d(s): 1,42,562 WARNING @ Sun, 02 Jun 2019 22:52:23: #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 22:52:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:52:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:52:26: 17000000 INFO @ Sun, 02 Jun 2019 22:52:28: 17000000 INFO @ Sun, 02 Jun 2019 22:52:30: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:52:30: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:52:30: #1 total tags in treatment: 17520437 INFO @ Sun, 02 Jun 2019 22:52:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:52:30: #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 22:52:30: #1 tags after filtering in treatment: 17520437 INFO @ Sun, 02 Jun 2019 22:52:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:52:30: #1 finished! INFO @ Sun, 02 Jun 2019 22:52:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:52:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:52:31: #2 number of paired peaks: 239 WARNING @ Sun, 02 Jun 2019 22:52:31: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Sun, 02 Jun 2019 22:52:31: start model_add_line... INFO @ Sun, 02 Jun 2019 22:52:32: start X-correlation... INFO @ Sun, 02 Jun 2019 22:52:32: end of X-cor INFO @ Sun, 02 Jun 2019 22:52:32: #2 finished! INFO @ Sun, 02 Jun 2019 22:52:32: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:52:32: #2 alternative fragment length(s) may be 1,42,562 bps INFO @ Sun, 02 Jun 2019 22:52:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.10_model.r WARNING @ Sun, 02 Jun 2019 22:52:32: #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 22:52:32: #2 You may need to consider one of the other alternative d(s): 1,42,562 WARNING @ Sun, 02 Jun 2019 22:52:32: #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 22:52:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:52:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:52:32: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:52:32: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:52:32: #1 total tags in treatment: 17520437 INFO @ Sun, 02 Jun 2019 22:52:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:52:32: #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 22:52:32: #1 tags after filtering in treatment: 17520437 INFO @ Sun, 02 Jun 2019 22:52:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:52:32: #1 finished! INFO @ Sun, 02 Jun 2019 22:52:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:52:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:52:34: #2 number of paired peaks: 239 WARNING @ Sun, 02 Jun 2019 22:52:34: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Sun, 02 Jun 2019 22:52:34: start model_add_line... INFO @ Sun, 02 Jun 2019 22:52:34: start X-correlation... INFO @ Sun, 02 Jun 2019 22:52:34: end of X-cor INFO @ Sun, 02 Jun 2019 22:52:34: #2 finished! INFO @ Sun, 02 Jun 2019 22:52:34: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:52:34: #2 alternative fragment length(s) may be 1,42,562 bps INFO @ Sun, 02 Jun 2019 22:52:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.20_model.r WARNING @ Sun, 02 Jun 2019 22:52:34: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:52:34: #2 You may need to consider one of the other alternative d(s): 1,42,562 WARNING @ Sun, 02 Jun 2019 22:52:34: #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 22:52:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:52:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:53:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:53:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:53:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:53:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:53:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:53:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.05_summits.bed INFO @ Sun, 02 Jun 2019 22:53:20: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:53:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:53:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:53:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.10_summits.bed INFO @ Sun, 02 Jun 2019 22:53:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:53:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:53:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:53:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402768/SRX5402768.20_summits.bed INFO @ Sun, 02 Jun 2019 22:53:32: 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。