Job ID = 1292331 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,914,899 reads read : 13,914,899 reads written : 13,914,899 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: 00:03:02 13914899 reads; of these: 13914899 (100.00%) were unpaired; of these: 1205351 (8.66%) aligned 0 times 10598386 (76.17%) aligned exactly 1 time 2111162 (15.17%) aligned >1 times 91.34% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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] 7123736 / 12709548 = 0.5605 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 18:08:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.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 18:08:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:08:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:08:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.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 18:08:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:08:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:08:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.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 18:08:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:08:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:08:12: 1000000 INFO @ Sun, 02 Jun 2019 18:08:12: 1000000 INFO @ Sun, 02 Jun 2019 18:08:13: 1000000 INFO @ Sun, 02 Jun 2019 18:08:20: 2000000 INFO @ Sun, 02 Jun 2019 18:08:20: 2000000 INFO @ Sun, 02 Jun 2019 18:08:22: 2000000 INFO @ Sun, 02 Jun 2019 18:08:29: 3000000 INFO @ Sun, 02 Jun 2019 18:08:29: 3000000 INFO @ Sun, 02 Jun 2019 18:08:31: 3000000 INFO @ Sun, 02 Jun 2019 18:08:37: 4000000 INFO @ Sun, 02 Jun 2019 18:08:37: 4000000 INFO @ Sun, 02 Jun 2019 18:08:40: 4000000 INFO @ Sun, 02 Jun 2019 18:08:45: 5000000 INFO @ Sun, 02 Jun 2019 18:08:46: 5000000 INFO @ Sun, 02 Jun 2019 18:08:49: 5000000 INFO @ Sun, 02 Jun 2019 18:08:50: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:08:50: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:08:50: #1 total tags in treatment: 5585812 INFO @ Sun, 02 Jun 2019 18:08:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:08:50: #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 18:08:50: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:08:50: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:08:50: #1 total tags in treatment: 5585812 INFO @ Sun, 02 Jun 2019 18:08:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:08:50: #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 18:08:50: #1 tags after filtering in treatment: 5585812 INFO @ Sun, 02 Jun 2019 18:08:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:08:50: #1 finished! INFO @ Sun, 02 Jun 2019 18:08:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:08:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:08:50: #1 tags after filtering in treatment: 5585812 INFO @ Sun, 02 Jun 2019 18:08:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:08:50: #1 finished! INFO @ Sun, 02 Jun 2019 18:08:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:08:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:08:51: #2 number of paired peaks: 579 WARNING @ Sun, 02 Jun 2019 18:08:51: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Sun, 02 Jun 2019 18:08:51: start model_add_line... INFO @ Sun, 02 Jun 2019 18:08:51: #2 number of paired peaks: 579 WARNING @ Sun, 02 Jun 2019 18:08:51: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Sun, 02 Jun 2019 18:08:51: start model_add_line... INFO @ Sun, 02 Jun 2019 18:08:51: start X-correlation... INFO @ Sun, 02 Jun 2019 18:08:51: end of X-cor INFO @ Sun, 02 Jun 2019 18:08:51: #2 finished! INFO @ Sun, 02 Jun 2019 18:08:51: #2 predicted fragment length is 42 bps INFO @ Sun, 02 Jun 2019 18:08:51: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 02 Jun 2019 18:08:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.20_model.r WARNING @ Sun, 02 Jun 2019 18:08:51: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:08:51: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 02 Jun 2019 18:08:51: #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 18:08:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:08:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:08:51: start X-correlation... INFO @ Sun, 02 Jun 2019 18:08:51: end of X-cor INFO @ Sun, 02 Jun 2019 18:08:51: #2 finished! INFO @ Sun, 02 Jun 2019 18:08:51: #2 predicted fragment length is 42 bps INFO @ Sun, 02 Jun 2019 18:08:51: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 02 Jun 2019 18:08:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.10_model.r WARNING @ Sun, 02 Jun 2019 18:08:51: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:08:51: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 02 Jun 2019 18:08:51: #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 18:08:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:08:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:08:54: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:08:54: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:08:54: #1 total tags in treatment: 5585812 INFO @ Sun, 02 Jun 2019 18:08:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:08:54: #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 18:08:54: #1 tags after filtering in treatment: 5585812 INFO @ Sun, 02 Jun 2019 18:08:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:08:54: #1 finished! INFO @ Sun, 02 Jun 2019 18:08:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:08:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:08:54: #2 number of paired peaks: 579 WARNING @ Sun, 02 Jun 2019 18:08:54: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Sun, 02 Jun 2019 18:08:54: start model_add_line... INFO @ Sun, 02 Jun 2019 18:08:54: start X-correlation... INFO @ Sun, 02 Jun 2019 18:08:54: end of X-cor INFO @ Sun, 02 Jun 2019 18:08:54: #2 finished! INFO @ Sun, 02 Jun 2019 18:08:54: #2 predicted fragment length is 42 bps INFO @ Sun, 02 Jun 2019 18:08:54: #2 alternative fragment length(s) may be 3,42 bps INFO @ Sun, 02 Jun 2019 18:08:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.05_model.r WARNING @ Sun, 02 Jun 2019 18:08:54: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:08:55: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Sun, 02 Jun 2019 18:08:55: #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 18:08:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:08:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:09:08: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:09:08: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:09:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:09:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:09:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:09:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.10_summits.bed INFO @ Sun, 02 Jun 2019 18:09:16: Done! INFO @ Sun, 02 Jun 2019 18:09:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.20_peaks.xls pass1 - making usageList (6 chroms): 1 millis INFO @ Sun, 02 Jun 2019 18:09:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.20_peaks.narrowPeak pass2 - checking and writing primary data (422 records, 4 fields): 2 millis INFO @ Sun, 02 Jun 2019 18:09:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.20_summits.bed INFO @ Sun, 02 Jun 2019 18:09:16: Done! CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:09:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:09:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:09:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331355/SRX331355.05_summits.bed INFO @ Sun, 02 Jun 2019 18:09:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (705 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。