Job ID = 1290604 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,961,380 reads read : 10,961,380 reads written : 10,961,380 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:59 10961380 reads; of these: 10961380 (100.00%) were unpaired; of these: 123983 (1.13%) aligned 0 times 9526842 (86.91%) aligned exactly 1 time 1310555 (11.96%) aligned >1 times 98.87% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1627600 / 10837397 = 0.1502 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 @ Sat, 01 Jun 2019 21:52:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.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 @ Sat, 01 Jun 2019 21:52:47: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:52:47: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:52:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.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 @ Sat, 01 Jun 2019 21:52:47: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:52:47: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:52:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.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 @ Sat, 01 Jun 2019 21:52:47: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:52:47: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:53:02: 1000000 INFO @ Sat, 01 Jun 2019 21:53:02: 1000000 INFO @ Sat, 01 Jun 2019 21:53:03: 1000000 INFO @ Sat, 01 Jun 2019 21:53:15: 2000000 INFO @ Sat, 01 Jun 2019 21:53:16: 2000000 INFO @ Sat, 01 Jun 2019 21:53:18: 2000000 INFO @ Sat, 01 Jun 2019 21:53:30: 3000000 INFO @ Sat, 01 Jun 2019 21:53:31: 3000000 INFO @ Sat, 01 Jun 2019 21:53:34: 3000000 INFO @ Sat, 01 Jun 2019 21:53:44: 4000000 INFO @ Sat, 01 Jun 2019 21:53:45: 4000000 INFO @ Sat, 01 Jun 2019 21:53:49: 4000000 INFO @ Sat, 01 Jun 2019 21:53:59: 5000000 INFO @ Sat, 01 Jun 2019 21:54:00: 5000000 INFO @ Sat, 01 Jun 2019 21:54:03: 5000000 INFO @ Sat, 01 Jun 2019 21:54:13: 6000000 INFO @ Sat, 01 Jun 2019 21:54:17: 6000000 INFO @ Sat, 01 Jun 2019 21:54:18: 6000000 INFO @ Sat, 01 Jun 2019 21:54:30: 7000000 INFO @ Sat, 01 Jun 2019 21:54:32: 7000000 INFO @ Sat, 01 Jun 2019 21:54:35: 7000000 INFO @ Sat, 01 Jun 2019 21:54:45: 8000000 INFO @ Sat, 01 Jun 2019 21:54:46: 8000000 INFO @ Sat, 01 Jun 2019 21:54:50: 8000000 INFO @ Sat, 01 Jun 2019 21:55:02: 9000000 INFO @ Sat, 01 Jun 2019 21:55:04: 9000000 INFO @ Sat, 01 Jun 2019 21:55:05: 9000000 INFO @ Sat, 01 Jun 2019 21:55:06: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:55:06: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:55:06: #1 total tags in treatment: 9209797 INFO @ Sat, 01 Jun 2019 21:55:06: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:55:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:55:06: #1 tags after filtering in treatment: 9209797 INFO @ Sat, 01 Jun 2019 21:55:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:55:06: #1 finished! INFO @ Sat, 01 Jun 2019 21:55:06: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:55:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:55:07: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:55:07: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:55:07: #1 total tags in treatment: 9209797 INFO @ Sat, 01 Jun 2019 21:55:07: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:55:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:55:07: #1 tags after filtering in treatment: 9209797 INFO @ Sat, 01 Jun 2019 21:55:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:55:07: #1 finished! INFO @ Sat, 01 Jun 2019 21:55:07: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:55:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:55:07: #2 number of paired peaks: 335 WARNING @ Sat, 01 Jun 2019 21:55:07: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sat, 01 Jun 2019 21:55:07: start model_add_line... INFO @ Sat, 01 Jun 2019 21:55:07: start X-correlation... INFO @ Sat, 01 Jun 2019 21:55:07: end of X-cor INFO @ Sat, 01 Jun 2019 21:55:07: #2 finished! INFO @ Sat, 01 Jun 2019 21:55:07: #2 predicted fragment length is 56 bps INFO @ Sat, 01 Jun 2019 21:55:07: #2 alternative fragment length(s) may be 3,56,128,532 bps INFO @ Sat, 01 Jun 2019 21:55:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.05_model.r WARNING @ Sat, 01 Jun 2019 21:55:07: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:55:07: #2 You may need to consider one of the other alternative d(s): 3,56,128,532 WARNING @ Sat, 01 Jun 2019 21:55:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:55:07: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:55:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:55:08: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:55:08: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:55:08: #1 total tags in treatment: 9209797 INFO @ Sat, 01 Jun 2019 21:55:08: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:55:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:55:08: #2 number of paired peaks: 335 WARNING @ Sat, 01 Jun 2019 21:55:08: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sat, 01 Jun 2019 21:55:08: start model_add_line... INFO @ Sat, 01 Jun 2019 21:55:08: #1 tags after filtering in treatment: 9209797 INFO @ Sat, 01 Jun 2019 21:55:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:55:08: #1 finished! INFO @ Sat, 01 Jun 2019 21:55:08: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:55:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:55:08: start X-correlation... INFO @ Sat, 01 Jun 2019 21:55:08: end of X-cor INFO @ Sat, 01 Jun 2019 21:55:08: #2 finished! INFO @ Sat, 01 Jun 2019 21:55:08: #2 predicted fragment length is 56 bps INFO @ Sat, 01 Jun 2019 21:55:08: #2 alternative fragment length(s) may be 3,56,128,532 bps INFO @ Sat, 01 Jun 2019 21:55:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.20_model.r WARNING @ Sat, 01 Jun 2019 21:55:08: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:55:08: #2 You may need to consider one of the other alternative d(s): 3,56,128,532 WARNING @ Sat, 01 Jun 2019 21:55:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:55:08: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:55:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:55:09: #2 number of paired peaks: 335 WARNING @ Sat, 01 Jun 2019 21:55:09: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sat, 01 Jun 2019 21:55:09: start model_add_line... INFO @ Sat, 01 Jun 2019 21:55:09: start X-correlation... INFO @ Sat, 01 Jun 2019 21:55:09: end of X-cor INFO @ Sat, 01 Jun 2019 21:55:09: #2 finished! INFO @ Sat, 01 Jun 2019 21:55:09: #2 predicted fragment length is 56 bps INFO @ Sat, 01 Jun 2019 21:55:09: #2 alternative fragment length(s) may be 3,56,128,532 bps INFO @ Sat, 01 Jun 2019 21:55:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.10_model.r WARNING @ Sat, 01 Jun 2019 21:55:09: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:55:09: #2 You may need to consider one of the other alternative d(s): 3,56,128,532 WARNING @ Sat, 01 Jun 2019 21:55:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:55:09: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:55:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:55:43: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:55:46: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:55:47: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:56:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:56:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:56:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.05_summits.bed INFO @ Sat, 01 Jun 2019 21:56:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (897 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:56:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:56:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:56:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.20_summits.bed INFO @ Sat, 01 Jun 2019 21:56:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (65 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:56:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:56:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:56:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350751/SRX2350751.10_summits.bed INFO @ Sat, 01 Jun 2019 21:56:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (183 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。