Job ID = 2589926 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,117,538 reads read : 20,117,538 reads written : 20,117,538 rm: cannot remove ‘[DSE]RR*’: 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: 00:04:46 20117538 reads; of these: 20117538 (100.00%) were unpaired; of these: 1022139 (5.08%) aligned 0 times 15666086 (77.87%) aligned exactly 1 time 3429313 (17.05%) aligned >1 times 94.92% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 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] 2624006 / 19095399 = 0.1374 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 @ Mon, 12 Aug 2019 19:08:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.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 @ Mon, 12 Aug 2019 19:08:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:08:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:08:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.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 @ Mon, 12 Aug 2019 19:08:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:08:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:08:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.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 @ Mon, 12 Aug 2019 19:08:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:08:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:08:14: 1000000 INFO @ Mon, 12 Aug 2019 19:08:15: 1000000 INFO @ Mon, 12 Aug 2019 19:08:15: 1000000 INFO @ Mon, 12 Aug 2019 19:08:21: 2000000 INFO @ Mon, 12 Aug 2019 19:08:22: 2000000 INFO @ Mon, 12 Aug 2019 19:08:22: 2000000 INFO @ Mon, 12 Aug 2019 19:08:28: 3000000 INFO @ Mon, 12 Aug 2019 19:08:30: 3000000 INFO @ Mon, 12 Aug 2019 19:08:30: 3000000 INFO @ Mon, 12 Aug 2019 19:08:34: 4000000 INFO @ Mon, 12 Aug 2019 19:08:38: 4000000 INFO @ Mon, 12 Aug 2019 19:08:38: 4000000 INFO @ Mon, 12 Aug 2019 19:08:41: 5000000 INFO @ Mon, 12 Aug 2019 19:08:46: 5000000 INFO @ Mon, 12 Aug 2019 19:08:46: 5000000 INFO @ Mon, 12 Aug 2019 19:08:47: 6000000 INFO @ Mon, 12 Aug 2019 19:08:53: 7000000 INFO @ Mon, 12 Aug 2019 19:08:53: 6000000 INFO @ Mon, 12 Aug 2019 19:08:54: 6000000 INFO @ Mon, 12 Aug 2019 19:09:00: 8000000 INFO @ Mon, 12 Aug 2019 19:09:01: 7000000 INFO @ Mon, 12 Aug 2019 19:09:01: 7000000 INFO @ Mon, 12 Aug 2019 19:09:06: 9000000 INFO @ Mon, 12 Aug 2019 19:09:08: 8000000 INFO @ Mon, 12 Aug 2019 19:09:09: 8000000 INFO @ Mon, 12 Aug 2019 19:09:12: 10000000 INFO @ Mon, 12 Aug 2019 19:09:16: 9000000 INFO @ Mon, 12 Aug 2019 19:09:17: 9000000 INFO @ Mon, 12 Aug 2019 19:09:19: 11000000 INFO @ Mon, 12 Aug 2019 19:09:23: 10000000 INFO @ Mon, 12 Aug 2019 19:09:24: 10000000 INFO @ Mon, 12 Aug 2019 19:09:25: 12000000 INFO @ Mon, 12 Aug 2019 19:09:30: 11000000 INFO @ Mon, 12 Aug 2019 19:09:31: 13000000 INFO @ Mon, 12 Aug 2019 19:09:32: 11000000 INFO @ Mon, 12 Aug 2019 19:09:38: 14000000 INFO @ Mon, 12 Aug 2019 19:09:38: 12000000 INFO @ Mon, 12 Aug 2019 19:09:39: 12000000 INFO @ Mon, 12 Aug 2019 19:09:44: 15000000 INFO @ Mon, 12 Aug 2019 19:09:45: 13000000 INFO @ Mon, 12 Aug 2019 19:09:47: 13000000 INFO @ Mon, 12 Aug 2019 19:09:50: 16000000 INFO @ Mon, 12 Aug 2019 19:09:53: 14000000 INFO @ Mon, 12 Aug 2019 19:09:53: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:09:53: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:09:53: #1 total tags in treatment: 16471393 INFO @ Mon, 12 Aug 2019 19:09:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:09:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:09:54: #1 tags after filtering in treatment: 16471393 INFO @ Mon, 12 Aug 2019 19:09:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:09:54: #1 finished! INFO @ Mon, 12 Aug 2019 19:09:54: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:09:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:09:55: 14000000 INFO @ Mon, 12 Aug 2019 19:09:55: #2 number of paired peaks: 241 WARNING @ Mon, 12 Aug 2019 19:09:55: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Mon, 12 Aug 2019 19:09:55: start model_add_line... INFO @ Mon, 12 Aug 2019 19:09:55: start X-correlation... INFO @ Mon, 12 Aug 2019 19:09:55: end of X-cor INFO @ Mon, 12 Aug 2019 19:09:55: #2 finished! INFO @ Mon, 12 Aug 2019 19:09:55: #2 predicted fragment length is 46 bps INFO @ Mon, 12 Aug 2019 19:09:55: #2 alternative fragment length(s) may be 2,46 bps INFO @ Mon, 12 Aug 2019 19:09:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.20_model.r WARNING @ Mon, 12 Aug 2019 19:09:55: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:09:55: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Mon, 12 Aug 2019 19:09:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:09:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:09:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:10:00: 15000000 INFO @ Mon, 12 Aug 2019 19:10:02: 15000000 INFO @ Mon, 12 Aug 2019 19:10:07: 16000000 INFO @ Mon, 12 Aug 2019 19:10:10: 16000000 INFO @ Mon, 12 Aug 2019 19:10:11: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:10:11: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:10:11: #1 total tags in treatment: 16471393 INFO @ Mon, 12 Aug 2019 19:10:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:10:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:10:11: #1 tags after filtering in treatment: 16471393 INFO @ Mon, 12 Aug 2019 19:10:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:10:11: #1 finished! INFO @ Mon, 12 Aug 2019 19:10:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:10:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:10:13: #2 number of paired peaks: 241 WARNING @ Mon, 12 Aug 2019 19:10:13: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Mon, 12 Aug 2019 19:10:13: start model_add_line... INFO @ Mon, 12 Aug 2019 19:10:13: start X-correlation... INFO @ Mon, 12 Aug 2019 19:10:13: end of X-cor INFO @ Mon, 12 Aug 2019 19:10:13: #2 finished! INFO @ Mon, 12 Aug 2019 19:10:13: #2 predicted fragment length is 46 bps INFO @ Mon, 12 Aug 2019 19:10:13: #2 alternative fragment length(s) may be 2,46 bps INFO @ Mon, 12 Aug 2019 19:10:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.10_model.r WARNING @ Mon, 12 Aug 2019 19:10:13: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:10:13: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Mon, 12 Aug 2019 19:10:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:10:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:10:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:10:13: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:10:13: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:10:13: #1 total tags in treatment: 16471393 INFO @ Mon, 12 Aug 2019 19:10:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:10:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:10:14: #1 tags after filtering in treatment: 16471393 INFO @ Mon, 12 Aug 2019 19:10:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:10:14: #1 finished! INFO @ Mon, 12 Aug 2019 19:10:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:10:15: #2 number of paired peaks: 241 WARNING @ Mon, 12 Aug 2019 19:10:15: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Mon, 12 Aug 2019 19:10:15: start model_add_line... INFO @ Mon, 12 Aug 2019 19:10:15: start X-correlation... INFO @ Mon, 12 Aug 2019 19:10:15: end of X-cor INFO @ Mon, 12 Aug 2019 19:10:15: #2 finished! INFO @ Mon, 12 Aug 2019 19:10:15: #2 predicted fragment length is 46 bps INFO @ Mon, 12 Aug 2019 19:10:15: #2 alternative fragment length(s) may be 2,46 bps INFO @ Mon, 12 Aug 2019 19:10:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.05_model.r WARNING @ Mon, 12 Aug 2019 19:10:15: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:10:15: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Mon, 12 Aug 2019 19:10:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:10:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:10:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:10:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:10:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:10:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:10:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:10:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.20_summits.bed INFO @ Mon, 12 Aug 2019 19:10:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (153 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:10:55: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:11:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:11:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:11:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.10_summits.bed INFO @ Mon, 12 Aug 2019 19:11:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (423 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:11:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:11:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:11:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331337/SRX331337.05_summits.bed INFO @ Mon, 12 Aug 2019 19:11:13: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (672 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。