Job ID = 1295687 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,234,913 reads read : 6,234,913 reads written : 6,234,913 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: 00:02:47 6234913 reads; of these: 6234913 (100.00%) were unpaired; of these: 941284 (15.10%) aligned 0 times 3467842 (55.62%) aligned exactly 1 time 1825787 (29.28%) aligned >1 times 84.90% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 558916 / 5293629 = 0.1056 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, 03 Jun 2019 15:01:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 15:01:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:01:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:01:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 15:01:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:01:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:01:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 15:01:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:01:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:01:36: 1000000 INFO @ Mon, 03 Jun 2019 15:01:36: 1000000 INFO @ Mon, 03 Jun 2019 15:01:37: 1000000 INFO @ Mon, 03 Jun 2019 15:01:43: 2000000 INFO @ Mon, 03 Jun 2019 15:01:44: 2000000 INFO @ Mon, 03 Jun 2019 15:01:45: 2000000 INFO @ Mon, 03 Jun 2019 15:01:50: 3000000 INFO @ Mon, 03 Jun 2019 15:01:51: 3000000 INFO @ Mon, 03 Jun 2019 15:01:53: 3000000 INFO @ Mon, 03 Jun 2019 15:01:57: 4000000 INFO @ Mon, 03 Jun 2019 15:01:59: 4000000 INFO @ Mon, 03 Jun 2019 15:02:01: 4000000 INFO @ Mon, 03 Jun 2019 15:02:03: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 15:02:03: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 15:02:03: #1 total tags in treatment: 4734713 INFO @ Mon, 03 Jun 2019 15:02:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:02:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:02:03: #1 tags after filtering in treatment: 4734713 INFO @ Mon, 03 Jun 2019 15:02:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:02:03: #1 finished! INFO @ Mon, 03 Jun 2019 15:02:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:02:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:02:03: #2 number of paired peaks: 552 WARNING @ Mon, 03 Jun 2019 15:02:03: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Mon, 03 Jun 2019 15:02:03: start model_add_line... INFO @ Mon, 03 Jun 2019 15:02:03: start X-correlation... INFO @ Mon, 03 Jun 2019 15:02:03: end of X-cor INFO @ Mon, 03 Jun 2019 15:02:03: #2 finished! INFO @ Mon, 03 Jun 2019 15:02:03: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 15:02:03: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 03 Jun 2019 15:02:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.20_model.r WARNING @ Mon, 03 Jun 2019 15:02:03: #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, 03 Jun 2019 15:02:03: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 03 Jun 2019 15:02:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 15:02:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:02:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:02:05: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 15:02:05: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 15:02:05: #1 total tags in treatment: 4734713 INFO @ Mon, 03 Jun 2019 15:02:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:02:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:02:05: #1 tags after filtering in treatment: 4734713 INFO @ Mon, 03 Jun 2019 15:02:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:02:05: #1 finished! INFO @ Mon, 03 Jun 2019 15:02:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:02:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:02:06: #2 number of paired peaks: 552 WARNING @ Mon, 03 Jun 2019 15:02:06: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Mon, 03 Jun 2019 15:02:06: start model_add_line... INFO @ Mon, 03 Jun 2019 15:02:06: start X-correlation... INFO @ Mon, 03 Jun 2019 15:02:06: end of X-cor INFO @ Mon, 03 Jun 2019 15:02:06: #2 finished! INFO @ Mon, 03 Jun 2019 15:02:06: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 15:02:06: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 03 Jun 2019 15:02:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.10_model.r WARNING @ Mon, 03 Jun 2019 15:02:06: #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, 03 Jun 2019 15:02:06: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 03 Jun 2019 15:02:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 15:02:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:02:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:02:07: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 15:02:07: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 15:02:07: #1 total tags in treatment: 4734713 INFO @ Mon, 03 Jun 2019 15:02:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:02:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:02:07: #1 tags after filtering in treatment: 4734713 INFO @ Mon, 03 Jun 2019 15:02:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:02:07: #1 finished! INFO @ Mon, 03 Jun 2019 15:02:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:02:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:02:08: #2 number of paired peaks: 552 WARNING @ Mon, 03 Jun 2019 15:02:08: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Mon, 03 Jun 2019 15:02:08: start model_add_line... INFO @ Mon, 03 Jun 2019 15:02:08: start X-correlation... INFO @ Mon, 03 Jun 2019 15:02:08: end of X-cor INFO @ Mon, 03 Jun 2019 15:02:08: #2 finished! INFO @ Mon, 03 Jun 2019 15:02:08: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 15:02:08: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 03 Jun 2019 15:02:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.05_model.r WARNING @ Mon, 03 Jun 2019 15:02:08: #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, 03 Jun 2019 15:02:08: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 03 Jun 2019 15:02:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 15:02:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:02:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:02:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:02:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:02:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:02:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:02:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:02:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.20_summits.bed INFO @ Mon, 03 Jun 2019 15:02:25: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (540 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.10_summits.bed INFO @ Mon, 03 Jun 2019 15:02:27: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (1002 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:02:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:02:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:02:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX403434/SRX403434.05_summits.bed INFO @ Mon, 03 Jun 2019 15:02:30: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1461 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。