Job ID = 1294619 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,669,837 reads read : 14,669,837 reads written : 14,669,837 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: 00:07:28 14669837 reads; of these: 14669837 (100.00%) were unpaired; of these: 752197 (5.13%) aligned 0 times 9408673 (64.14%) aligned exactly 1 time 4508967 (30.74%) aligned >1 times 94.87% overall alignment rate Time searching: 00:07:28 Overall time: 00:07:28 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 8 files... [bam_rmdupse_core] 2630283 / 13917640 = 0.1890 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 09:34:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.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 09:34:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:34:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:34:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.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 09:34:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:34:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:34:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.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 09:34:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:34:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:34:22: 1000000 INFO @ Mon, 03 Jun 2019 09:34:22: 1000000 INFO @ Mon, 03 Jun 2019 09:34:24: 1000000 INFO @ Mon, 03 Jun 2019 09:34:32: 2000000 INFO @ Mon, 03 Jun 2019 09:34:32: 2000000 INFO @ Mon, 03 Jun 2019 09:34:35: 2000000 INFO @ Mon, 03 Jun 2019 09:34:40: 3000000 INFO @ Mon, 03 Jun 2019 09:34:40: 3000000 INFO @ Mon, 03 Jun 2019 09:34:45: 3000000 INFO @ Mon, 03 Jun 2019 09:34:48: 4000000 INFO @ Mon, 03 Jun 2019 09:34:49: 4000000 INFO @ Mon, 03 Jun 2019 09:34:55: 4000000 INFO @ Mon, 03 Jun 2019 09:34:57: 5000000 INFO @ Mon, 03 Jun 2019 09:34:58: 5000000 INFO @ Mon, 03 Jun 2019 09:35:05: 5000000 INFO @ Mon, 03 Jun 2019 09:35:05: 6000000 INFO @ Mon, 03 Jun 2019 09:35:06: 6000000 INFO @ Mon, 03 Jun 2019 09:35:13: 7000000 INFO @ Mon, 03 Jun 2019 09:35:15: 6000000 INFO @ Mon, 03 Jun 2019 09:35:15: 7000000 INFO @ Mon, 03 Jun 2019 09:35:21: 8000000 INFO @ Mon, 03 Jun 2019 09:35:24: 8000000 INFO @ Mon, 03 Jun 2019 09:35:25: 7000000 INFO @ Mon, 03 Jun 2019 09:35:29: 9000000 INFO @ Mon, 03 Jun 2019 09:35:33: 9000000 INFO @ Mon, 03 Jun 2019 09:35:36: 8000000 INFO @ Mon, 03 Jun 2019 09:35:39: 10000000 INFO @ Mon, 03 Jun 2019 09:35:42: 10000000 INFO @ Mon, 03 Jun 2019 09:35:46: 9000000 INFO @ Mon, 03 Jun 2019 09:35:47: 11000000 INFO @ Mon, 03 Jun 2019 09:35:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:35:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:35:50: #1 total tags in treatment: 11287357 INFO @ Mon, 03 Jun 2019 09:35:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:35:50: #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 09:35:50: #1 tags after filtering in treatment: 11287357 INFO @ Mon, 03 Jun 2019 09:35:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:35:50: #1 finished! INFO @ Mon, 03 Jun 2019 09:35:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:35:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:35:50: 11000000 INFO @ Mon, 03 Jun 2019 09:35:51: #2 number of paired peaks: 476 WARNING @ Mon, 03 Jun 2019 09:35:51: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Mon, 03 Jun 2019 09:35:51: start model_add_line... INFO @ Mon, 03 Jun 2019 09:35:51: start X-correlation... INFO @ Mon, 03 Jun 2019 09:35:51: end of X-cor INFO @ Mon, 03 Jun 2019 09:35:51: #2 finished! INFO @ Mon, 03 Jun 2019 09:35:51: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 09:35:51: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 09:35:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.20_model.r WARNING @ Mon, 03 Jun 2019 09:35:51: #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 09:35:51: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 09:35:51: #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 09:35:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:35:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:35:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:35:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:35:53: #1 total tags in treatment: 11287357 INFO @ Mon, 03 Jun 2019 09:35:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:35:53: #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 09:35:53: #1 tags after filtering in treatment: 11287357 INFO @ Mon, 03 Jun 2019 09:35:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:35:53: #1 finished! INFO @ Mon, 03 Jun 2019 09:35:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:35:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:35:54: #2 number of paired peaks: 476 WARNING @ Mon, 03 Jun 2019 09:35:54: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Mon, 03 Jun 2019 09:35:54: start model_add_line... INFO @ Mon, 03 Jun 2019 09:35:54: start X-correlation... INFO @ Mon, 03 Jun 2019 09:35:54: end of X-cor INFO @ Mon, 03 Jun 2019 09:35:54: #2 finished! INFO @ Mon, 03 Jun 2019 09:35:54: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 09:35:54: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 09:35:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.05_model.r WARNING @ Mon, 03 Jun 2019 09:35:54: #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 09:35:54: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 09:35:54: #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 09:35:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:35:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:35:56: 10000000 INFO @ Mon, 03 Jun 2019 09:36:05: 11000000 INFO @ Mon, 03 Jun 2019 09:36:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:36:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:36:08: #1 total tags in treatment: 11287357 INFO @ Mon, 03 Jun 2019 09:36:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:36:08: #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 09:36:08: #1 tags after filtering in treatment: 11287357 INFO @ Mon, 03 Jun 2019 09:36:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:36:08: #1 finished! INFO @ Mon, 03 Jun 2019 09:36:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:36:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:36:10: #2 number of paired peaks: 476 WARNING @ Mon, 03 Jun 2019 09:36:10: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Mon, 03 Jun 2019 09:36:10: start model_add_line... INFO @ Mon, 03 Jun 2019 09:36:10: start X-correlation... INFO @ Mon, 03 Jun 2019 09:36:10: end of X-cor INFO @ Mon, 03 Jun 2019 09:36:10: #2 finished! INFO @ Mon, 03 Jun 2019 09:36:10: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 09:36:10: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 09:36:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.10_model.r WARNING @ Mon, 03 Jun 2019 09:36:10: #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 09:36:10: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 09:36:10: #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 09:36:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:36:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:36:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:36:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:36:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:36:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:36:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.20_summits.bed INFO @ Mon, 03 Jun 2019 09:36:37: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1137 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:36:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:36:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:36:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.05_summits.bed INFO @ Mon, 03 Jun 2019 09:36:40: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1700 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:36:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:36:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:36:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:36:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287784/SRX287784.10_summits.bed INFO @ Mon, 03 Jun 2019 09:36:57: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1477 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。