Job ID = 2589359 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,860,662 reads read : 11,860,662 reads written : 11,860,662 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: 00:02:55 11860662 reads; of these: 11860662 (100.00%) were unpaired; of these: 268520 (2.26%) aligned 0 times 9581749 (80.79%) aligned exactly 1 time 2010393 (16.95%) aligned >1 times 97.74% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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] 1199381 / 11592142 = 0.1035 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 17:42:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.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 17:42:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:42:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:42:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.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 17:42:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:42:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:42:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.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 17:42:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:42:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:42:28: 1000000 INFO @ Mon, 12 Aug 2019 17:42:33: 1000000 INFO @ Mon, 12 Aug 2019 17:42:34: 1000000 INFO @ Mon, 12 Aug 2019 17:42:36: 2000000 INFO @ Mon, 12 Aug 2019 17:42:43: 2000000 INFO @ Mon, 12 Aug 2019 17:42:43: 3000000 INFO @ Mon, 12 Aug 2019 17:42:44: 2000000 INFO @ Mon, 12 Aug 2019 17:42:50: 4000000 INFO @ Mon, 12 Aug 2019 17:42:52: 3000000 INFO @ Mon, 12 Aug 2019 17:42:54: 3000000 INFO @ Mon, 12 Aug 2019 17:42:57: 5000000 INFO @ Mon, 12 Aug 2019 17:43:02: 4000000 INFO @ Mon, 12 Aug 2019 17:43:03: 4000000 INFO @ Mon, 12 Aug 2019 17:43:04: 6000000 INFO @ Mon, 12 Aug 2019 17:43:11: 7000000 INFO @ Mon, 12 Aug 2019 17:43:12: 5000000 INFO @ Mon, 12 Aug 2019 17:43:13: 5000000 INFO @ Mon, 12 Aug 2019 17:43:18: 8000000 INFO @ Mon, 12 Aug 2019 17:43:21: 6000000 INFO @ Mon, 12 Aug 2019 17:43:23: 6000000 INFO @ Mon, 12 Aug 2019 17:43:25: 9000000 INFO @ Mon, 12 Aug 2019 17:43:31: 7000000 INFO @ Mon, 12 Aug 2019 17:43:32: 10000000 INFO @ Mon, 12 Aug 2019 17:43:33: 7000000 INFO @ Mon, 12 Aug 2019 17:43:35: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:43:35: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:43:35: #1 total tags in treatment: 10392761 INFO @ Mon, 12 Aug 2019 17:43:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:43:35: #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 17:43:35: #1 tags after filtering in treatment: 10392761 INFO @ Mon, 12 Aug 2019 17:43:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:43:35: #1 finished! INFO @ Mon, 12 Aug 2019 17:43:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:43:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:43:36: #2 number of paired peaks: 405 WARNING @ Mon, 12 Aug 2019 17:43:36: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Mon, 12 Aug 2019 17:43:36: start model_add_line... INFO @ Mon, 12 Aug 2019 17:43:36: start X-correlation... INFO @ Mon, 12 Aug 2019 17:43:36: end of X-cor INFO @ Mon, 12 Aug 2019 17:43:36: #2 finished! INFO @ Mon, 12 Aug 2019 17:43:36: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 17:43:36: #2 alternative fragment length(s) may be 2,53 bps INFO @ Mon, 12 Aug 2019 17:43:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.05_model.r WARNING @ Mon, 12 Aug 2019 17:43:36: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:43:36: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Mon, 12 Aug 2019 17:43:36: #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 17:43:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:43:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:43:41: 8000000 INFO @ Mon, 12 Aug 2019 17:43:42: 8000000 INFO @ Mon, 12 Aug 2019 17:43:50: 9000000 INFO @ Mon, 12 Aug 2019 17:43:52: 9000000 INFO @ Mon, 12 Aug 2019 17:44:00: 10000000 INFO @ Mon, 12 Aug 2019 17:44:01: 10000000 INFO @ Mon, 12 Aug 2019 17:44:04: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:44:04: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:44:04: #1 total tags in treatment: 10392761 INFO @ Mon, 12 Aug 2019 17:44:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:44:04: #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 17:44:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:44:04: #1 tags after filtering in treatment: 10392761 INFO @ Mon, 12 Aug 2019 17:44:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:44:04: #1 finished! INFO @ Mon, 12 Aug 2019 17:44:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:44:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:44:05: #2 number of paired peaks: 405 WARNING @ Mon, 12 Aug 2019 17:44:05: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Mon, 12 Aug 2019 17:44:05: start model_add_line... INFO @ Mon, 12 Aug 2019 17:44:05: start X-correlation... INFO @ Mon, 12 Aug 2019 17:44:05: end of X-cor INFO @ Mon, 12 Aug 2019 17:44:05: #2 finished! INFO @ Mon, 12 Aug 2019 17:44:05: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 17:44:05: #2 alternative fragment length(s) may be 2,53 bps INFO @ Mon, 12 Aug 2019 17:44:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.10_model.r WARNING @ Mon, 12 Aug 2019 17:44:05: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:44:05: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Mon, 12 Aug 2019 17:44:05: #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 17:44:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:44:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:44:05: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:44:05: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:44:05: #1 total tags in treatment: 10392761 INFO @ Mon, 12 Aug 2019 17:44:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:44:05: #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 17:44:05: #1 tags after filtering in treatment: 10392761 INFO @ Mon, 12 Aug 2019 17:44:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:44:05: #1 finished! INFO @ Mon, 12 Aug 2019 17:44:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:44:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:44:06: #2 number of paired peaks: 405 WARNING @ Mon, 12 Aug 2019 17:44:06: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Mon, 12 Aug 2019 17:44:06: start model_add_line... INFO @ Mon, 12 Aug 2019 17:44:06: start X-correlation... INFO @ Mon, 12 Aug 2019 17:44:06: end of X-cor INFO @ Mon, 12 Aug 2019 17:44:06: #2 finished! INFO @ Mon, 12 Aug 2019 17:44:06: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 17:44:06: #2 alternative fragment length(s) may be 2,53 bps INFO @ Mon, 12 Aug 2019 17:44:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.20_model.r WARNING @ Mon, 12 Aug 2019 17:44:06: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:44:06: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Mon, 12 Aug 2019 17:44:06: #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 17:44:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:44:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:44:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:44:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:44:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.05_summits.bed INFO @ Mon, 12 Aug 2019 17:44:17: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (680 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:44:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:44:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:44:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:44:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:44:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.10_summits.bed INFO @ Mon, 12 Aug 2019 17:44:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (411 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:44:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:44:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:44:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078712/SRX1078712.20_summits.bed INFO @ Mon, 12 Aug 2019 17:44:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。