Job ID = 2589686 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,598,253 reads read : 9,598,253 reads written : 9,598,253 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947287.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: 00:01:48 9598253 reads; of these: 9598253 (100.00%) were unpaired; of these: 367567 (3.83%) aligned 0 times 7356135 (76.64%) aligned exactly 1 time 1874551 (19.53%) aligned >1 times 96.17% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 1469987 / 9230686 = 0.1593 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 18:18:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.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 18:18:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:18:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:18:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.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 18:18:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:18:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:18:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.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 18:18:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:18:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:18:18: 1000000 INFO @ Mon, 12 Aug 2019 18:18:19: 1000000 INFO @ Mon, 12 Aug 2019 18:18:22: 1000000 INFO @ Mon, 12 Aug 2019 18:18:25: 2000000 INFO @ Mon, 12 Aug 2019 18:18:25: 2000000 INFO @ Mon, 12 Aug 2019 18:18:30: 2000000 INFO @ Mon, 12 Aug 2019 18:18:32: 3000000 INFO @ Mon, 12 Aug 2019 18:18:32: 3000000 INFO @ Mon, 12 Aug 2019 18:18:38: 4000000 INFO @ Mon, 12 Aug 2019 18:18:39: 4000000 INFO @ Mon, 12 Aug 2019 18:18:39: 3000000 INFO @ Mon, 12 Aug 2019 18:18:45: 5000000 INFO @ Mon, 12 Aug 2019 18:18:45: 5000000 INFO @ Mon, 12 Aug 2019 18:18:47: 4000000 INFO @ Mon, 12 Aug 2019 18:18:52: 6000000 INFO @ Mon, 12 Aug 2019 18:18:52: 6000000 INFO @ Mon, 12 Aug 2019 18:18:56: 5000000 INFO @ Mon, 12 Aug 2019 18:18:59: 7000000 INFO @ Mon, 12 Aug 2019 18:18:59: 7000000 INFO @ Mon, 12 Aug 2019 18:19:04: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:19:04: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:19:04: #1 total tags in treatment: 7760699 INFO @ Mon, 12 Aug 2019 18:19:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:19:04: #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 18:19:04: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:19:04: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:19:04: #1 total tags in treatment: 7760699 INFO @ Mon, 12 Aug 2019 18:19:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:19:04: #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 18:19:04: #1 tags after filtering in treatment: 7760699 INFO @ Mon, 12 Aug 2019 18:19:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:19:04: #1 finished! INFO @ Mon, 12 Aug 2019 18:19:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:19:04: #1 tags after filtering in treatment: 7760699 INFO @ Mon, 12 Aug 2019 18:19:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:19:04: #1 finished! INFO @ Mon, 12 Aug 2019 18:19:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:19:05: 6000000 INFO @ Mon, 12 Aug 2019 18:19:05: #2 number of paired peaks: 477 WARNING @ Mon, 12 Aug 2019 18:19:05: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Mon, 12 Aug 2019 18:19:05: start model_add_line... INFO @ Mon, 12 Aug 2019 18:19:05: start X-correlation... INFO @ Mon, 12 Aug 2019 18:19:05: #2 number of paired peaks: 477 WARNING @ Mon, 12 Aug 2019 18:19:05: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Mon, 12 Aug 2019 18:19:05: start model_add_line... INFO @ Mon, 12 Aug 2019 18:19:05: end of X-cor INFO @ Mon, 12 Aug 2019 18:19:05: #2 finished! INFO @ Mon, 12 Aug 2019 18:19:05: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:19:05: #2 alternative fragment length(s) may be 1,23 bps INFO @ Mon, 12 Aug 2019 18:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.05_model.r WARNING @ Mon, 12 Aug 2019 18:19:05: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:19:05: #2 You may need to consider one of the other alternative d(s): 1,23 WARNING @ Mon, 12 Aug 2019 18:19:05: #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 18:19:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:19:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:19:05: start X-correlation... INFO @ Mon, 12 Aug 2019 18:19:05: end of X-cor INFO @ Mon, 12 Aug 2019 18:19:05: #2 finished! INFO @ Mon, 12 Aug 2019 18:19:05: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:19:05: #2 alternative fragment length(s) may be 1,23 bps INFO @ Mon, 12 Aug 2019 18:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.10_model.r WARNING @ Mon, 12 Aug 2019 18:19:05: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:19:05: #2 You may need to consider one of the other alternative d(s): 1,23 WARNING @ Mon, 12 Aug 2019 18:19:05: #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 18:19:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:19:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:19:13: 7000000 INFO @ Mon, 12 Aug 2019 18:19:19: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:19:19: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:19:19: #1 total tags in treatment: 7760699 INFO @ Mon, 12 Aug 2019 18:19:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:19:19: #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 18:19:19: #1 tags after filtering in treatment: 7760699 INFO @ Mon, 12 Aug 2019 18:19:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:19:19: #1 finished! INFO @ Mon, 12 Aug 2019 18:19:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:19:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:19:20: #2 number of paired peaks: 477 WARNING @ Mon, 12 Aug 2019 18:19:20: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Mon, 12 Aug 2019 18:19:20: start model_add_line... INFO @ Mon, 12 Aug 2019 18:19:20: start X-correlation... INFO @ Mon, 12 Aug 2019 18:19:20: end of X-cor INFO @ Mon, 12 Aug 2019 18:19:20: #2 finished! INFO @ Mon, 12 Aug 2019 18:19:20: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:19:20: #2 alternative fragment length(s) may be 1,23 bps INFO @ Mon, 12 Aug 2019 18:19:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.20_model.r WARNING @ Mon, 12 Aug 2019 18:19:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:19:20: #2 You may need to consider one of the other alternative d(s): 1,23 WARNING @ Mon, 12 Aug 2019 18:19:20: #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 18:19:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:19:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:19:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:19:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:19:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:19:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:19:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.10_summits.bed INFO @ Mon, 12 Aug 2019 18:19:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:19:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:19:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:19:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.05_summits.bed INFO @ Mon, 12 Aug 2019 18:19:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:19:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:19:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:19:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:19:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331063/SRX331063.20_summits.bed INFO @ Mon, 12 Aug 2019 18:19:50: 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。