Job ID = 1303259 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,078,010 reads read : 28,078,010 reads written : 28,078,010 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: 00:12:53 28078010 reads; of these: 28078010 (100.00%) were unpaired; of these: 681580 (2.43%) aligned 0 times 19417005 (69.15%) aligned exactly 1 time 7979425 (28.42%) aligned >1 times 97.57% overall alignment rate Time searching: 00:12:53 Overall time: 00:12:53 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_sort_core] merging from 12 files... [bam_rmdupse_core] 3930197 / 27396430 = 0.1435 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 20:51:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.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 20:51:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:51:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:51:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.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 20:51:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:51:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:51:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.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 20:51:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:51:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:51:17: 1000000 INFO @ Mon, 03 Jun 2019 20:51:17: 1000000 INFO @ Mon, 03 Jun 2019 20:51:17: 1000000 INFO @ Mon, 03 Jun 2019 20:51:24: 2000000 INFO @ Mon, 03 Jun 2019 20:51:25: 2000000 INFO @ Mon, 03 Jun 2019 20:51:25: 2000000 INFO @ Mon, 03 Jun 2019 20:51:31: 3000000 INFO @ Mon, 03 Jun 2019 20:51:32: 3000000 INFO @ Mon, 03 Jun 2019 20:51:33: 3000000 INFO @ Mon, 03 Jun 2019 20:51:39: 4000000 INFO @ Mon, 03 Jun 2019 20:51:40: 4000000 INFO @ Mon, 03 Jun 2019 20:51:40: 4000000 INFO @ Mon, 03 Jun 2019 20:51:46: 5000000 INFO @ Mon, 03 Jun 2019 20:51:48: 5000000 INFO @ Mon, 03 Jun 2019 20:51:48: 5000000 INFO @ Mon, 03 Jun 2019 20:51:54: 6000000 INFO @ Mon, 03 Jun 2019 20:51:55: 6000000 INFO @ Mon, 03 Jun 2019 20:51:56: 6000000 INFO @ Mon, 03 Jun 2019 20:52:01: 7000000 INFO @ Mon, 03 Jun 2019 20:52:03: 7000000 INFO @ Mon, 03 Jun 2019 20:52:03: 7000000 INFO @ Mon, 03 Jun 2019 20:52:09: 8000000 INFO @ Mon, 03 Jun 2019 20:52:11: 8000000 INFO @ Mon, 03 Jun 2019 20:52:11: 8000000 INFO @ Mon, 03 Jun 2019 20:52:17: 9000000 INFO @ Mon, 03 Jun 2019 20:52:19: 9000000 INFO @ Mon, 03 Jun 2019 20:52:19: 9000000 INFO @ Mon, 03 Jun 2019 20:52:24: 10000000 INFO @ Mon, 03 Jun 2019 20:52:26: 10000000 INFO @ Mon, 03 Jun 2019 20:52:26: 10000000 INFO @ Mon, 03 Jun 2019 20:52:32: 11000000 INFO @ Mon, 03 Jun 2019 20:52:34: 11000000 INFO @ Mon, 03 Jun 2019 20:52:34: 11000000 INFO @ Mon, 03 Jun 2019 20:52:39: 12000000 INFO @ Mon, 03 Jun 2019 20:52:42: 12000000 INFO @ Mon, 03 Jun 2019 20:52:42: 12000000 INFO @ Mon, 03 Jun 2019 20:52:47: 13000000 INFO @ Mon, 03 Jun 2019 20:52:49: 13000000 INFO @ Mon, 03 Jun 2019 20:52:49: 13000000 INFO @ Mon, 03 Jun 2019 20:52:54: 14000000 INFO @ Mon, 03 Jun 2019 20:52:57: 14000000 INFO @ Mon, 03 Jun 2019 20:52:58: 14000000 INFO @ Mon, 03 Jun 2019 20:53:01: 15000000 INFO @ Mon, 03 Jun 2019 20:53:04: 15000000 INFO @ Mon, 03 Jun 2019 20:53:06: 15000000 INFO @ Mon, 03 Jun 2019 20:53:09: 16000000 INFO @ Mon, 03 Jun 2019 20:53:12: 16000000 INFO @ Mon, 03 Jun 2019 20:53:13: 16000000 INFO @ Mon, 03 Jun 2019 20:53:17: 17000000 INFO @ Mon, 03 Jun 2019 20:53:19: 17000000 INFO @ Mon, 03 Jun 2019 20:53:20: 17000000 INFO @ Mon, 03 Jun 2019 20:53:24: 18000000 INFO @ Mon, 03 Jun 2019 20:53:27: 18000000 INFO @ Mon, 03 Jun 2019 20:53:28: 18000000 INFO @ Mon, 03 Jun 2019 20:53:31: 19000000 INFO @ Mon, 03 Jun 2019 20:53:34: 19000000 INFO @ Mon, 03 Jun 2019 20:53:35: 19000000 INFO @ Mon, 03 Jun 2019 20:53:39: 20000000 INFO @ Mon, 03 Jun 2019 20:53:42: 20000000 INFO @ Mon, 03 Jun 2019 20:53:42: 20000000 INFO @ Mon, 03 Jun 2019 20:53:46: 21000000 INFO @ Mon, 03 Jun 2019 20:53:49: 21000000 INFO @ Mon, 03 Jun 2019 20:53:50: 21000000 INFO @ Mon, 03 Jun 2019 20:53:54: 22000000 INFO @ Mon, 03 Jun 2019 20:53:57: 22000000 INFO @ Mon, 03 Jun 2019 20:53:57: 22000000 INFO @ Mon, 03 Jun 2019 20:54:01: 23000000 INFO @ Mon, 03 Jun 2019 20:54:05: 23000000 INFO @ Mon, 03 Jun 2019 20:54:05: 23000000 INFO @ Mon, 03 Jun 2019 20:54:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:54:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:54:05: #1 total tags in treatment: 23466233 INFO @ Mon, 03 Jun 2019 20:54:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:54:05: #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 20:54:06: #1 tags after filtering in treatment: 23466233 INFO @ Mon, 03 Jun 2019 20:54:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:54:06: #1 finished! INFO @ Mon, 03 Jun 2019 20:54:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:54:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:54:08: #2 number of paired peaks: 110 WARNING @ Mon, 03 Jun 2019 20:54:08: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Mon, 03 Jun 2019 20:54:08: start model_add_line... INFO @ Mon, 03 Jun 2019 20:54:08: start X-correlation... INFO @ Mon, 03 Jun 2019 20:54:08: end of X-cor INFO @ Mon, 03 Jun 2019 20:54:08: #2 finished! INFO @ Mon, 03 Jun 2019 20:54:08: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 20:54:08: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 20:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.20_model.r WARNING @ Mon, 03 Jun 2019 20:54:08: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:54:08: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 20:54:08: #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 20:54:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:54:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:54:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:54:08: #1 total tags in treatment: 23466233 INFO @ Mon, 03 Jun 2019 20:54:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:54:08: #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 20:54:09: #1 tags after filtering in treatment: 23466233 INFO @ Mon, 03 Jun 2019 20:54:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:54:09: #1 finished! INFO @ Mon, 03 Jun 2019 20:54:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:54:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:54:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:54:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:54:09: #1 total tags in treatment: 23466233 INFO @ Mon, 03 Jun 2019 20:54:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:54:09: #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 20:54:09: #1 tags after filtering in treatment: 23466233 INFO @ Mon, 03 Jun 2019 20:54:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:54:09: #1 finished! INFO @ Mon, 03 Jun 2019 20:54:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:54:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:54:10: #2 number of paired peaks: 110 WARNING @ Mon, 03 Jun 2019 20:54:10: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Mon, 03 Jun 2019 20:54:10: start model_add_line... INFO @ Mon, 03 Jun 2019 20:54:11: start X-correlation... INFO @ Mon, 03 Jun 2019 20:54:11: end of X-cor INFO @ Mon, 03 Jun 2019 20:54:11: #2 finished! INFO @ Mon, 03 Jun 2019 20:54:11: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 20:54:11: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 20:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.10_model.r WARNING @ Mon, 03 Jun 2019 20:54:11: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:54:11: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 20:54:11: #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 20:54:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:54:11: #2 number of paired peaks: 110 WARNING @ Mon, 03 Jun 2019 20:54:11: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Mon, 03 Jun 2019 20:54:11: start model_add_line... INFO @ Mon, 03 Jun 2019 20:54:11: start X-correlation... INFO @ Mon, 03 Jun 2019 20:54:11: end of X-cor INFO @ Mon, 03 Jun 2019 20:54:11: #2 finished! INFO @ Mon, 03 Jun 2019 20:54:11: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 20:54:11: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 20:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.05_model.r WARNING @ Mon, 03 Jun 2019 20:54:11: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:54:11: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 20:54:11: #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 20:54:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:55:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:55:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:55:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:55:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:55:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:55:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.20_summits.bed INFO @ Mon, 03 Jun 2019 20:55:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1120 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:55:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:55:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:55:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.05_summits.bed INFO @ Mon, 03 Jun 2019 20:55:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1790 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:55:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:55:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:55:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933902/SRX4933902.10_summits.bed INFO @ Mon, 03 Jun 2019 20:55:33: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1469 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。