Job ID = 1293183 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,575,875 reads read : 23,575,875 reads written : 23,575,875 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:04:04 23575875 reads; of these: 23575875 (100.00%) were unpaired; of these: 15518033 (65.82%) aligned 0 times 4961641 (21.05%) aligned exactly 1 time 3096201 (13.13%) aligned >1 times 34.18% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 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] 1669345 / 8057842 = 0.2072 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 22:25:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.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 22:25:31: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:25:31: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:25:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.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 22:25:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:25:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:25:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.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 22:25:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:25:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:25:40: 1000000 INFO @ Sun, 02 Jun 2019 22:25:40: 1000000 INFO @ Sun, 02 Jun 2019 22:25:40: 1000000 INFO @ Sun, 02 Jun 2019 22:25:48: 2000000 INFO @ Sun, 02 Jun 2019 22:25:48: 2000000 INFO @ Sun, 02 Jun 2019 22:25:49: 2000000 INFO @ Sun, 02 Jun 2019 22:25:56: 3000000 INFO @ Sun, 02 Jun 2019 22:25:57: 3000000 INFO @ Sun, 02 Jun 2019 22:25:57: 3000000 INFO @ Sun, 02 Jun 2019 22:26:04: 4000000 INFO @ Sun, 02 Jun 2019 22:26:05: 4000000 INFO @ Sun, 02 Jun 2019 22:26:05: 4000000 INFO @ Sun, 02 Jun 2019 22:26:12: 5000000 INFO @ Sun, 02 Jun 2019 22:26:12: 5000000 INFO @ Sun, 02 Jun 2019 22:26:13: 5000000 INFO @ Sun, 02 Jun 2019 22:26:20: 6000000 INFO @ Sun, 02 Jun 2019 22:26:20: 6000000 INFO @ Sun, 02 Jun 2019 22:26:21: 6000000 INFO @ Sun, 02 Jun 2019 22:26:23: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:26:23: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:26:23: #1 total tags in treatment: 6388497 INFO @ Sun, 02 Jun 2019 22:26:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:26:23: #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 22:26:23: #1 tags after filtering in treatment: 6388497 INFO @ Sun, 02 Jun 2019 22:26:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:26:23: #1 finished! INFO @ Sun, 02 Jun 2019 22:26:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:26:23: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:26:23: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:26:23: #1 total tags in treatment: 6388497 INFO @ Sun, 02 Jun 2019 22:26:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:26:23: #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 22:26:24: #1 tags after filtering in treatment: 6388497 INFO @ Sun, 02 Jun 2019 22:26:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:26:24: #1 finished! INFO @ Sun, 02 Jun 2019 22:26:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:26:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:26:24: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:26:24: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:26:24: #1 total tags in treatment: 6388497 INFO @ Sun, 02 Jun 2019 22:26:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:26:24: #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 22:26:24: #1 tags after filtering in treatment: 6388497 INFO @ Sun, 02 Jun 2019 22:26:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:26:24: #1 finished! INFO @ Sun, 02 Jun 2019 22:26:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:26:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:26:24: #2 number of paired peaks: 1706 INFO @ Sun, 02 Jun 2019 22:26:24: start model_add_line... INFO @ Sun, 02 Jun 2019 22:26:24: start X-correlation... INFO @ Sun, 02 Jun 2019 22:26:24: end of X-cor INFO @ Sun, 02 Jun 2019 22:26:24: #2 finished! INFO @ Sun, 02 Jun 2019 22:26:24: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 22:26:24: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sun, 02 Jun 2019 22:26:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.10_model.r WARNING @ Sun, 02 Jun 2019 22:26:24: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:26:24: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sun, 02 Jun 2019 22:26:24: #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 22:26:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:26:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:26:24: #2 number of paired peaks: 1706 INFO @ Sun, 02 Jun 2019 22:26:24: start model_add_line... INFO @ Sun, 02 Jun 2019 22:26:24: start X-correlation... INFO @ Sun, 02 Jun 2019 22:26:24: end of X-cor INFO @ Sun, 02 Jun 2019 22:26:24: #2 finished! INFO @ Sun, 02 Jun 2019 22:26:24: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 22:26:24: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sun, 02 Jun 2019 22:26:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.20_model.r WARNING @ Sun, 02 Jun 2019 22:26:24: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:26:24: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sun, 02 Jun 2019 22:26:24: #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 22:26:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:26:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:26:25: #2 number of paired peaks: 1706 INFO @ Sun, 02 Jun 2019 22:26:25: start model_add_line... INFO @ Sun, 02 Jun 2019 22:26:25: start X-correlation... INFO @ Sun, 02 Jun 2019 22:26:25: end of X-cor INFO @ Sun, 02 Jun 2019 22:26:25: #2 finished! INFO @ Sun, 02 Jun 2019 22:26:25: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 22:26:25: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sun, 02 Jun 2019 22:26:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.05_model.r WARNING @ Sun, 02 Jun 2019 22:26:25: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:26:25: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sun, 02 Jun 2019 22:26:25: #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 22:26:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:26:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:26:43: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:26:43: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:26:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:26:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:26:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:26:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.10_summits.bed INFO @ Sun, 02 Jun 2019 22:26:52: Done! pass1 - making usageList (6 chroms): 2 millis INFO @ Sun, 02 Jun 2019 22:26:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.20_peaks.xls pass2 - checking and writing primary data (1100 records, 4 fields): 7 millis INFO @ Sun, 02 Jun 2019 22:26:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:26:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.20_summits.bed INFO @ Sun, 02 Jun 2019 22:26:52: Done! CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (359 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:26:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:26:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:26:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402743/SRX5402743.05_summits.bed INFO @ Sun, 02 Jun 2019 22:26:53: Done! pass1 - making usageList (6 chroms): 5 millis pass2 - checking and writing primary data (2724 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。