Job ID = 2589838 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,853,525 reads read : 7,853,525 reads written : 7,853,525 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947467.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: 00:01:35 7853525 reads; of these: 7853525 (100.00%) were unpaired; of these: 155057 (1.97%) aligned 0 times 6218810 (79.18%) aligned exactly 1 time 1479658 (18.84%) aligned >1 times 98.03% overall alignment rate Time searching: 00:01:35 Overall time: 00:01:35 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] 1121826 / 7698468 = 0.1457 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 18:37:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.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 18:37:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:37:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:37:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.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 18:37:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:37:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:37:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.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 18:37:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:37:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:37:34: 1000000 INFO @ Mon, 12 Aug 2019 18:37:34: 1000000 INFO @ Mon, 12 Aug 2019 18:37:37: 1000000 INFO @ Mon, 12 Aug 2019 18:37:40: 2000000 INFO @ Mon, 12 Aug 2019 18:37:43: 2000000 INFO @ Mon, 12 Aug 2019 18:37:46: 2000000 INFO @ Mon, 12 Aug 2019 18:37:47: 3000000 INFO @ Mon, 12 Aug 2019 18:37:52: 3000000 INFO @ Mon, 12 Aug 2019 18:37:53: 4000000 INFO @ Mon, 12 Aug 2019 18:37:55: 3000000 INFO @ Mon, 12 Aug 2019 18:38:00: 5000000 INFO @ Mon, 12 Aug 2019 18:38:01: 4000000 INFO @ Mon, 12 Aug 2019 18:38:04: 4000000 INFO @ Mon, 12 Aug 2019 18:38:06: 6000000 INFO @ Mon, 12 Aug 2019 18:38:10: 5000000 INFO @ Mon, 12 Aug 2019 18:38:10: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:38:10: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:38:10: #1 total tags in treatment: 6576642 INFO @ Mon, 12 Aug 2019 18:38:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:38:10: #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 18:38:10: #1 tags after filtering in treatment: 6576642 INFO @ Mon, 12 Aug 2019 18:38:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:38:10: #1 finished! INFO @ Mon, 12 Aug 2019 18:38:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:38:11: #2 number of paired peaks: 507 WARNING @ Mon, 12 Aug 2019 18:38:11: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Mon, 12 Aug 2019 18:38:11: start model_add_line... INFO @ Mon, 12 Aug 2019 18:38:11: start X-correlation... INFO @ Mon, 12 Aug 2019 18:38:11: end of X-cor INFO @ Mon, 12 Aug 2019 18:38:11: #2 finished! INFO @ Mon, 12 Aug 2019 18:38:11: #2 predicted fragment length is 26 bps INFO @ Mon, 12 Aug 2019 18:38:11: #2 alternative fragment length(s) may be 2,26,507,513 bps INFO @ Mon, 12 Aug 2019 18:38:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.10_model.r WARNING @ Mon, 12 Aug 2019 18:38:11: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:38:11: #2 You may need to consider one of the other alternative d(s): 2,26,507,513 WARNING @ Mon, 12 Aug 2019 18:38:11: #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 18:38:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:38:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:38:12: 5000000 INFO @ Mon, 12 Aug 2019 18:38:18: 6000000 INFO @ Mon, 12 Aug 2019 18:38:21: 6000000 INFO @ Mon, 12 Aug 2019 18:38:23: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:38:23: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:38:23: #1 total tags in treatment: 6576642 INFO @ Mon, 12 Aug 2019 18:38:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:38:23: #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 18:38:23: #1 tags after filtering in treatment: 6576642 INFO @ Mon, 12 Aug 2019 18:38:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:38:23: #1 finished! INFO @ Mon, 12 Aug 2019 18:38:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:38:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:38:24: #2 number of paired peaks: 507 WARNING @ Mon, 12 Aug 2019 18:38:24: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Mon, 12 Aug 2019 18:38:24: start model_add_line... INFO @ Mon, 12 Aug 2019 18:38:24: start X-correlation... INFO @ Mon, 12 Aug 2019 18:38:24: end of X-cor INFO @ Mon, 12 Aug 2019 18:38:24: #2 finished! INFO @ Mon, 12 Aug 2019 18:38:24: #2 predicted fragment length is 26 bps INFO @ Mon, 12 Aug 2019 18:38:24: #2 alternative fragment length(s) may be 2,26,507,513 bps INFO @ Mon, 12 Aug 2019 18:38:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.05_model.r WARNING @ Mon, 12 Aug 2019 18:38:24: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:38:24: #2 You may need to consider one of the other alternative d(s): 2,26,507,513 WARNING @ Mon, 12 Aug 2019 18:38:24: #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 18:38:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:38:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:38:26: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:38:26: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:38:26: #1 total tags in treatment: 6576642 INFO @ Mon, 12 Aug 2019 18:38:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:38:26: #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 18:38:26: #1 tags after filtering in treatment: 6576642 INFO @ Mon, 12 Aug 2019 18:38:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:38:26: #1 finished! INFO @ Mon, 12 Aug 2019 18:38:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:38:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:38:26: #2 number of paired peaks: 507 WARNING @ Mon, 12 Aug 2019 18:38:26: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Mon, 12 Aug 2019 18:38:26: start model_add_line... INFO @ Mon, 12 Aug 2019 18:38:27: start X-correlation... INFO @ Mon, 12 Aug 2019 18:38:27: end of X-cor INFO @ Mon, 12 Aug 2019 18:38:27: #2 finished! INFO @ Mon, 12 Aug 2019 18:38:27: #2 predicted fragment length is 26 bps INFO @ Mon, 12 Aug 2019 18:38:27: #2 alternative fragment length(s) may be 2,26,507,513 bps INFO @ Mon, 12 Aug 2019 18:38:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.20_model.r WARNING @ Mon, 12 Aug 2019 18:38:27: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:38:27: #2 You may need to consider one of the other alternative d(s): 2,26,507,513 WARNING @ Mon, 12 Aug 2019 18:38:27: #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 18:38:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:38:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:38:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:38:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:38:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:38:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.10_summits.bed INFO @ Mon, 12 Aug 2019 18:38:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (232 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:38:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:38:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:38:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:38:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:38:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.05_summits.bed INFO @ Mon, 12 Aug 2019 18:38:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (540 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:38:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:38:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:38:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331235/SRX331235.20_summits.bed INFO @ Mon, 12 Aug 2019 18:38:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (17 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。