Job ID = 1295187 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,559,305 reads read : 21,559,305 reads written : 21,559,305 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: 00:09:06 21559305 reads; of these: 21559305 (100.00%) were unpaired; of these: 1335741 (6.20%) aligned 0 times 15428650 (71.56%) aligned exactly 1 time 4794914 (22.24%) aligned >1 times 93.80% overall alignment rate Time searching: 00:09:06 Overall time: 00:09:06 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] 1890349 / 20223564 = 0.0935 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 12:51:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.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 12:51:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:51:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:51:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.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 12:51:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:51:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:51:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.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 12:51:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:51:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:52:03: 1000000 INFO @ Mon, 03 Jun 2019 12:52:04: 1000000 INFO @ Mon, 03 Jun 2019 12:52:05: 1000000 INFO @ Mon, 03 Jun 2019 12:52:13: 2000000 INFO @ Mon, 03 Jun 2019 12:52:15: 2000000 INFO @ Mon, 03 Jun 2019 12:52:17: 2000000 INFO @ Mon, 03 Jun 2019 12:52:23: 3000000 INFO @ Mon, 03 Jun 2019 12:52:26: 3000000 INFO @ Mon, 03 Jun 2019 12:52:28: 3000000 INFO @ Mon, 03 Jun 2019 12:52:33: 4000000 INFO @ Mon, 03 Jun 2019 12:52:36: 4000000 INFO @ Mon, 03 Jun 2019 12:52:40: 4000000 INFO @ Mon, 03 Jun 2019 12:52:43: 5000000 INFO @ Mon, 03 Jun 2019 12:52:48: 5000000 INFO @ Mon, 03 Jun 2019 12:52:52: 5000000 INFO @ Mon, 03 Jun 2019 12:52:53: 6000000 INFO @ Mon, 03 Jun 2019 12:52:58: 6000000 INFO @ Mon, 03 Jun 2019 12:53:03: 7000000 INFO @ Mon, 03 Jun 2019 12:53:04: 6000000 INFO @ Mon, 03 Jun 2019 12:53:09: 7000000 INFO @ Mon, 03 Jun 2019 12:53:12: 8000000 INFO @ Mon, 03 Jun 2019 12:53:15: 7000000 INFO @ Mon, 03 Jun 2019 12:53:20: 8000000 INFO @ Mon, 03 Jun 2019 12:53:22: 9000000 INFO @ Mon, 03 Jun 2019 12:53:25: 8000000 INFO @ Mon, 03 Jun 2019 12:53:30: 9000000 INFO @ Mon, 03 Jun 2019 12:53:32: 10000000 INFO @ Mon, 03 Jun 2019 12:53:36: 9000000 INFO @ Mon, 03 Jun 2019 12:53:41: 10000000 INFO @ Mon, 03 Jun 2019 12:53:42: 11000000 INFO @ Mon, 03 Jun 2019 12:53:48: 10000000 INFO @ Mon, 03 Jun 2019 12:53:52: 12000000 INFO @ Mon, 03 Jun 2019 12:53:52: 11000000 INFO @ Mon, 03 Jun 2019 12:54:00: 11000000 INFO @ Mon, 03 Jun 2019 12:54:02: 13000000 INFO @ Mon, 03 Jun 2019 12:54:03: 12000000 INFO @ Mon, 03 Jun 2019 12:54:11: 12000000 INFO @ Mon, 03 Jun 2019 12:54:11: 14000000 INFO @ Mon, 03 Jun 2019 12:54:13: 13000000 INFO @ Mon, 03 Jun 2019 12:54:21: 15000000 INFO @ Mon, 03 Jun 2019 12:54:23: 13000000 INFO @ Mon, 03 Jun 2019 12:54:24: 14000000 INFO @ Mon, 03 Jun 2019 12:54:30: 16000000 INFO @ Mon, 03 Jun 2019 12:54:34: 14000000 INFO @ Mon, 03 Jun 2019 12:54:34: 15000000 INFO @ Mon, 03 Jun 2019 12:54:40: 17000000 INFO @ Mon, 03 Jun 2019 12:54:45: 16000000 INFO @ Mon, 03 Jun 2019 12:54:45: 15000000 INFO @ Mon, 03 Jun 2019 12:54:50: 18000000 INFO @ Mon, 03 Jun 2019 12:54:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:54:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:54:53: #1 total tags in treatment: 18333215 INFO @ Mon, 03 Jun 2019 12:54:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:54:53: #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 12:54:53: #1 tags after filtering in treatment: 18333215 INFO @ Mon, 03 Jun 2019 12:54:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:54:53: #1 finished! INFO @ Mon, 03 Jun 2019 12:54:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:54:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:54:55: #2 number of paired peaks: 161 WARNING @ Mon, 03 Jun 2019 12:54:55: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Mon, 03 Jun 2019 12:54:55: start model_add_line... INFO @ Mon, 03 Jun 2019 12:54:55: start X-correlation... INFO @ Mon, 03 Jun 2019 12:54:55: end of X-cor INFO @ Mon, 03 Jun 2019 12:54:55: #2 finished! INFO @ Mon, 03 Jun 2019 12:54:55: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 12:54:55: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 12:54:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.10_model.r WARNING @ Mon, 03 Jun 2019 12:54:55: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:54:55: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 12:54:55: #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 12:54:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:54:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:54:55: 17000000 INFO @ Mon, 03 Jun 2019 12:54:56: 16000000 INFO @ Mon, 03 Jun 2019 12:55:06: 18000000 INFO @ Mon, 03 Jun 2019 12:55:07: 17000000 INFO @ Mon, 03 Jun 2019 12:55:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:55:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:55:09: #1 total tags in treatment: 18333215 INFO @ Mon, 03 Jun 2019 12:55:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:55:09: #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 12:55:09: #1 tags after filtering in treatment: 18333215 INFO @ Mon, 03 Jun 2019 12:55:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:55:09: #1 finished! INFO @ Mon, 03 Jun 2019 12:55:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:55:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:55:11: #2 number of paired peaks: 161 WARNING @ Mon, 03 Jun 2019 12:55:11: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Mon, 03 Jun 2019 12:55:11: start model_add_line... INFO @ Mon, 03 Jun 2019 12:55:11: start X-correlation... INFO @ Mon, 03 Jun 2019 12:55:11: end of X-cor INFO @ Mon, 03 Jun 2019 12:55:11: #2 finished! INFO @ Mon, 03 Jun 2019 12:55:11: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 12:55:11: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 12:55:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.20_model.r WARNING @ Mon, 03 Jun 2019 12:55:11: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:55:11: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 12:55:11: #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 12:55:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:55:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:55:18: 18000000 INFO @ Mon, 03 Jun 2019 12:55:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:55:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:55:22: #1 total tags in treatment: 18333215 INFO @ Mon, 03 Jun 2019 12:55:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:55:22: #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 12:55:22: #1 tags after filtering in treatment: 18333215 INFO @ Mon, 03 Jun 2019 12:55:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:55:22: #1 finished! INFO @ Mon, 03 Jun 2019 12:55:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:55:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:55:24: #2 number of paired peaks: 161 WARNING @ Mon, 03 Jun 2019 12:55:24: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Mon, 03 Jun 2019 12:55:24: start model_add_line... INFO @ Mon, 03 Jun 2019 12:55:24: start X-correlation... INFO @ Mon, 03 Jun 2019 12:55:24: end of X-cor INFO @ Mon, 03 Jun 2019 12:55:24: #2 finished! INFO @ Mon, 03 Jun 2019 12:55:24: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 12:55:24: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 12:55:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.05_model.r WARNING @ Mon, 03 Jun 2019 12:55:24: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:55:24: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 12:55:24: #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 12:55:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:55:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:55:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:55:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:56:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:56:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:56:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.10_summits.bed INFO @ Mon, 03 Jun 2019 12:56:06: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1617 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:56:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:56:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:56:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:56:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.20_summits.bed INFO @ Mon, 03 Jun 2019 12:56:24: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1081 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:56:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:56:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:56:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331374/SRX331374.05_summits.bed INFO @ Mon, 03 Jun 2019 12:56:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1987 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。