Job ID = 1292390 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,727,694 reads read : 5,727,694 reads written : 5,727,694 spots read : 5,615,844 reads read : 5,615,844 reads written : 5,615,844 rm: cannot remove ‘fastqDump_tmp*’: 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 11343538 reads; of these: 11343538 (100.00%) were unpaired; of these: 1235720 (10.89%) aligned 0 times 8463647 (74.61%) aligned exactly 1 time 1644171 (14.49%) aligned >1 times 89.11% 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] 927448 / 10107818 = 0.0918 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 @ Sun, 02 Jun 2019 18:16:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.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 @ Sun, 02 Jun 2019 18:16:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:16:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:16:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.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 @ Sun, 02 Jun 2019 18:16:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:16:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:16:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.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 @ Sun, 02 Jun 2019 18:16:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:16:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:16:25: 1000000 INFO @ Sun, 02 Jun 2019 18:16:25: 1000000 INFO @ Sun, 02 Jun 2019 18:16:26: 1000000 INFO @ Sun, 02 Jun 2019 18:16:32: 2000000 INFO @ Sun, 02 Jun 2019 18:16:32: 2000000 INFO @ Sun, 02 Jun 2019 18:16:32: 2000000 INFO @ Sun, 02 Jun 2019 18:16:38: 3000000 INFO @ Sun, 02 Jun 2019 18:16:39: 3000000 INFO @ Sun, 02 Jun 2019 18:16:39: 3000000 INFO @ Sun, 02 Jun 2019 18:16:44: 4000000 INFO @ Sun, 02 Jun 2019 18:16:45: 4000000 INFO @ Sun, 02 Jun 2019 18:16:45: 4000000 INFO @ Sun, 02 Jun 2019 18:16:50: 5000000 INFO @ Sun, 02 Jun 2019 18:16:51: 5000000 INFO @ Sun, 02 Jun 2019 18:16:52: 5000000 INFO @ Sun, 02 Jun 2019 18:16:56: 6000000 INFO @ Sun, 02 Jun 2019 18:16:57: 6000000 INFO @ Sun, 02 Jun 2019 18:16:58: 6000000 INFO @ Sun, 02 Jun 2019 18:17:02: 7000000 INFO @ Sun, 02 Jun 2019 18:17:03: 7000000 INFO @ Sun, 02 Jun 2019 18:17:04: 7000000 INFO @ Sun, 02 Jun 2019 18:17:08: 8000000 INFO @ Sun, 02 Jun 2019 18:17:09: 8000000 INFO @ Sun, 02 Jun 2019 18:17:11: 8000000 INFO @ Sun, 02 Jun 2019 18:17:14: 9000000 INFO @ Sun, 02 Jun 2019 18:17:15: 9000000 INFO @ Sun, 02 Jun 2019 18:17:15: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 18:17:15: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 18:17:15: #1 total tags in treatment: 9180370 INFO @ Sun, 02 Jun 2019 18:17:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:17:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:17:15: #1 tags after filtering in treatment: 9180370 INFO @ Sun, 02 Jun 2019 18:17:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:17:15: #1 finished! INFO @ Sun, 02 Jun 2019 18:17:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:17:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:17:16: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 18:17:16: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 18:17:16: #1 total tags in treatment: 9180370 INFO @ Sun, 02 Jun 2019 18:17:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:17:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:17:16: #2 number of paired peaks: 322 WARNING @ Sun, 02 Jun 2019 18:17:16: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Sun, 02 Jun 2019 18:17:16: start model_add_line... INFO @ Sun, 02 Jun 2019 18:17:16: #1 tags after filtering in treatment: 9180370 INFO @ Sun, 02 Jun 2019 18:17:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:17:16: #1 finished! INFO @ Sun, 02 Jun 2019 18:17:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:17:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:17:16: start X-correlation... INFO @ Sun, 02 Jun 2019 18:17:16: end of X-cor INFO @ Sun, 02 Jun 2019 18:17:16: #2 finished! INFO @ Sun, 02 Jun 2019 18:17:16: #2 predicted fragment length is 29 bps INFO @ Sun, 02 Jun 2019 18:17:16: #2 alternative fragment length(s) may be 2,29,502,528,554,584 bps INFO @ Sun, 02 Jun 2019 18:17:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.05_model.r WARNING @ Sun, 02 Jun 2019 18:17:16: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:17:16: #2 You may need to consider one of the other alternative d(s): 2,29,502,528,554,584 WARNING @ Sun, 02 Jun 2019 18:17:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:17:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:17:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:17:17: #2 number of paired peaks: 322 WARNING @ Sun, 02 Jun 2019 18:17:17: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Sun, 02 Jun 2019 18:17:17: start model_add_line... INFO @ Sun, 02 Jun 2019 18:17:17: start X-correlation... INFO @ Sun, 02 Jun 2019 18:17:17: end of X-cor INFO @ Sun, 02 Jun 2019 18:17:17: #2 finished! INFO @ Sun, 02 Jun 2019 18:17:17: #2 predicted fragment length is 29 bps INFO @ Sun, 02 Jun 2019 18:17:17: #2 alternative fragment length(s) may be 2,29,502,528,554,584 bps INFO @ Sun, 02 Jun 2019 18:17:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.10_model.r WARNING @ Sun, 02 Jun 2019 18:17:17: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:17:17: #2 You may need to consider one of the other alternative d(s): 2,29,502,528,554,584 WARNING @ Sun, 02 Jun 2019 18:17:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:17:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:17:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:17:17: 9000000 INFO @ Sun, 02 Jun 2019 18:17:18: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 18:17:18: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 18:17:18: #1 total tags in treatment: 9180370 INFO @ Sun, 02 Jun 2019 18:17:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:17:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:17:19: #1 tags after filtering in treatment: 9180370 INFO @ Sun, 02 Jun 2019 18:17:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:17:19: #1 finished! INFO @ Sun, 02 Jun 2019 18:17:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:17:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:17:19: #2 number of paired peaks: 322 WARNING @ Sun, 02 Jun 2019 18:17:19: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Sun, 02 Jun 2019 18:17:19: start model_add_line... INFO @ Sun, 02 Jun 2019 18:17:19: start X-correlation... INFO @ Sun, 02 Jun 2019 18:17:19: end of X-cor INFO @ Sun, 02 Jun 2019 18:17:19: #2 finished! INFO @ Sun, 02 Jun 2019 18:17:19: #2 predicted fragment length is 29 bps INFO @ Sun, 02 Jun 2019 18:17:19: #2 alternative fragment length(s) may be 2,29,502,528,554,584 bps INFO @ Sun, 02 Jun 2019 18:17:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.20_model.r WARNING @ Sun, 02 Jun 2019 18:17:19: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:17:19: #2 You may need to consider one of the other alternative d(s): 2,29,502,528,554,584 WARNING @ Sun, 02 Jun 2019 18:17:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:17:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:17:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:17:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:17:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:17:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:17:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:17:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:17:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.05_summits.bed INFO @ Sun, 02 Jun 2019 18:17:53: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (566 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:17:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:17:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:17:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.10_summits.bed INFO @ Sun, 02 Jun 2019 18:17:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (258 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:17:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:17:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:17:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX395524/SRX395524.20_summits.bed INFO @ Sun, 02 Jun 2019 18:17:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (61 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。