Job ID = 2589507 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,279,839 reads read : 9,279,839 reads written : 9,279,839 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR660144.sra.cache’: 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: 00:01:49 9279839 reads; of these: 9279839 (100.00%) were unpaired; of these: 564197 (6.08%) aligned 0 times 7374594 (79.47%) aligned exactly 1 time 1341048 (14.45%) aligned >1 times 93.92% overall alignment rate Time searching: 00:01:49 Overall time: 00:01:49 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_rmdupse_core] 715111 / 8715642 = 0.0820 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 17:53:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.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 17:53:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.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 17:53:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.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 17:53:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:53:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:53:20: 1000000 INFO @ Mon, 12 Aug 2019 17:53:21: 1000000 INFO @ Mon, 12 Aug 2019 17:53:22: 1000000 INFO @ Mon, 12 Aug 2019 17:53:27: 2000000 INFO @ Mon, 12 Aug 2019 17:53:28: 2000000 INFO @ Mon, 12 Aug 2019 17:53:29: 2000000 INFO @ Mon, 12 Aug 2019 17:53:34: 3000000 INFO @ Mon, 12 Aug 2019 17:53:34: 3000000 INFO @ Mon, 12 Aug 2019 17:53:37: 3000000 INFO @ Mon, 12 Aug 2019 17:53:41: 4000000 INFO @ Mon, 12 Aug 2019 17:53:42: 4000000 INFO @ Mon, 12 Aug 2019 17:53:44: 4000000 INFO @ Mon, 12 Aug 2019 17:53:48: 5000000 INFO @ Mon, 12 Aug 2019 17:53:49: 5000000 INFO @ Mon, 12 Aug 2019 17:53:52: 5000000 INFO @ Mon, 12 Aug 2019 17:53:54: 6000000 INFO @ Mon, 12 Aug 2019 17:53:57: 6000000 INFO @ Mon, 12 Aug 2019 17:53:59: 6000000 INFO @ Mon, 12 Aug 2019 17:54:01: 7000000 INFO @ Mon, 12 Aug 2019 17:54:04: 7000000 INFO @ Mon, 12 Aug 2019 17:54:06: 7000000 INFO @ Mon, 12 Aug 2019 17:54:07: 8000000 INFO @ Mon, 12 Aug 2019 17:54:08: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:08: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:08: #1 total tags in treatment: 8000531 INFO @ Mon, 12 Aug 2019 17:54:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:08: #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 17:54:08: #1 tags after filtering in treatment: 8000531 INFO @ Mon, 12 Aug 2019 17:54:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:08: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:08: #2 number of paired peaks: 384 WARNING @ Mon, 12 Aug 2019 17:54:08: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:08: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:09: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:09: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:09: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:09: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 17:54:09: #2 alternative fragment length(s) may be 2,34,520,577,596,598 bps INFO @ Mon, 12 Aug 2019 17:54:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.10_model.r WARNING @ Mon, 12 Aug 2019 17:54:09: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:54:09: #2 You may need to consider one of the other alternative d(s): 2,34,520,577,596,598 WARNING @ Mon, 12 Aug 2019 17:54:09: #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 17:54:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:11: 8000000 INFO @ Mon, 12 Aug 2019 17:54:11: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:11: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:11: #1 total tags in treatment: 8000531 INFO @ Mon, 12 Aug 2019 17:54:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:11: #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 17:54:11: #1 tags after filtering in treatment: 8000531 INFO @ Mon, 12 Aug 2019 17:54:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:11: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:12: #2 number of paired peaks: 384 WARNING @ Mon, 12 Aug 2019 17:54:12: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:12: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:12: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:12: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:12: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:12: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 17:54:12: #2 alternative fragment length(s) may be 2,34,520,577,596,598 bps INFO @ Mon, 12 Aug 2019 17:54:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.05_model.r WARNING @ Mon, 12 Aug 2019 17:54:12: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:54:12: #2 You may need to consider one of the other alternative d(s): 2,34,520,577,596,598 WARNING @ Mon, 12 Aug 2019 17:54:12: #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 17:54:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:13: 8000000 INFO @ Mon, 12 Aug 2019 17:54:13: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:13: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:13: #1 total tags in treatment: 8000531 INFO @ Mon, 12 Aug 2019 17:54:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:13: #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 17:54:13: #1 tags after filtering in treatment: 8000531 INFO @ Mon, 12 Aug 2019 17:54:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:13: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:14: #2 number of paired peaks: 384 WARNING @ Mon, 12 Aug 2019 17:54:14: Fewer paired peaks (384) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 384 pairs to build model! INFO @ Mon, 12 Aug 2019 17:54:14: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:14: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:14: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:14: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:14: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 17:54:14: #2 alternative fragment length(s) may be 2,34,520,577,596,598 bps INFO @ Mon, 12 Aug 2019 17:54:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.20_model.r WARNING @ Mon, 12 Aug 2019 17:54:14: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:54:14: #2 You may need to consider one of the other alternative d(s): 2,34,520,577,596,598 WARNING @ Mon, 12 Aug 2019 17:54:14: #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 17:54:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.10_summits.bed INFO @ Mon, 12 Aug 2019 17:54:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (271 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:54:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.05_summits.bed INFO @ Mon, 12 Aug 2019 17:54:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (585 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:54:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX222637/SRX222637.20_summits.bed INFO @ Mon, 12 Aug 2019 17:54:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (78 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。