Job ID = 1294952 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,374,099 reads read : 13,374,099 reads written : 13,374,099 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: 00:06:52 13374099 reads; of these: 13374099 (100.00%) were unpaired; of these: 933104 (6.98%) aligned 0 times 5981622 (44.73%) aligned exactly 1 time 6459373 (48.30%) aligned >1 times 93.02% overall alignment rate Time searching: 00:06:52 Overall time: 00:06:52 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] 1694864 / 12440995 = 0.1362 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 11:10:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.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 11:10:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:10:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:10:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.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 11:10:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:10:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:10:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.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 11:10:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:10:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:10:22: 1000000 INFO @ Mon, 03 Jun 2019 11:10:23: 1000000 INFO @ Mon, 03 Jun 2019 11:10:25: 1000000 INFO @ Mon, 03 Jun 2019 11:10:30: 2000000 INFO @ Mon, 03 Jun 2019 11:10:31: 2000000 INFO @ Mon, 03 Jun 2019 11:10:36: 2000000 INFO @ Mon, 03 Jun 2019 11:10:37: 3000000 INFO @ Mon, 03 Jun 2019 11:10:40: 3000000 INFO @ Mon, 03 Jun 2019 11:10:45: 4000000 INFO @ Mon, 03 Jun 2019 11:10:47: 3000000 INFO @ Mon, 03 Jun 2019 11:10:48: 4000000 INFO @ Mon, 03 Jun 2019 11:10:53: 5000000 INFO @ Mon, 03 Jun 2019 11:10:57: 5000000 INFO @ Mon, 03 Jun 2019 11:10:58: 4000000 INFO @ Mon, 03 Jun 2019 11:11:02: 6000000 INFO @ Mon, 03 Jun 2019 11:11:07: 6000000 INFO @ Mon, 03 Jun 2019 11:11:10: 5000000 INFO @ Mon, 03 Jun 2019 11:11:10: 7000000 INFO @ Mon, 03 Jun 2019 11:11:16: 7000000 INFO @ Mon, 03 Jun 2019 11:11:18: 8000000 INFO @ Mon, 03 Jun 2019 11:11:21: 6000000 INFO @ Mon, 03 Jun 2019 11:11:25: 8000000 INFO @ Mon, 03 Jun 2019 11:11:26: 9000000 INFO @ Mon, 03 Jun 2019 11:11:33: 7000000 INFO @ Mon, 03 Jun 2019 11:11:34: 10000000 INFO @ Mon, 03 Jun 2019 11:11:34: 9000000 INFO @ Mon, 03 Jun 2019 11:11:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:11:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:11:40: #1 total tags in treatment: 10746131 INFO @ Mon, 03 Jun 2019 11:11:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:11:40: #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 11:11:40: #1 tags after filtering in treatment: 10746131 INFO @ Mon, 03 Jun 2019 11:11:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:11:40: #1 finished! INFO @ Mon, 03 Jun 2019 11:11:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:11:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:11:41: #2 number of paired peaks: 800 WARNING @ Mon, 03 Jun 2019 11:11:41: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Mon, 03 Jun 2019 11:11:41: start model_add_line... INFO @ Mon, 03 Jun 2019 11:11:41: start X-correlation... INFO @ Mon, 03 Jun 2019 11:11:41: end of X-cor INFO @ Mon, 03 Jun 2019 11:11:41: #2 finished! INFO @ Mon, 03 Jun 2019 11:11:41: #2 predicted fragment length is 87 bps INFO @ Mon, 03 Jun 2019 11:11:41: #2 alternative fragment length(s) may be 87 bps INFO @ Mon, 03 Jun 2019 11:11:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.05_model.r WARNING @ Mon, 03 Jun 2019 11:11:41: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:11:41: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Mon, 03 Jun 2019 11:11:41: #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 11:11:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:11:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:11:43: 10000000 INFO @ Mon, 03 Jun 2019 11:11:44: 8000000 INFO @ Mon, 03 Jun 2019 11:11:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:11:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:11:50: #1 total tags in treatment: 10746131 INFO @ Mon, 03 Jun 2019 11:11:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:11:50: #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 11:11:50: #1 tags after filtering in treatment: 10746131 INFO @ Mon, 03 Jun 2019 11:11:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:11:50: #1 finished! INFO @ Mon, 03 Jun 2019 11:11:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:11:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:11:51: #2 number of paired peaks: 800 WARNING @ Mon, 03 Jun 2019 11:11:51: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Mon, 03 Jun 2019 11:11:51: start model_add_line... INFO @ Mon, 03 Jun 2019 11:11:52: start X-correlation... INFO @ Mon, 03 Jun 2019 11:11:52: end of X-cor INFO @ Mon, 03 Jun 2019 11:11:52: #2 finished! INFO @ Mon, 03 Jun 2019 11:11:52: #2 predicted fragment length is 87 bps INFO @ Mon, 03 Jun 2019 11:11:52: #2 alternative fragment length(s) may be 87 bps INFO @ Mon, 03 Jun 2019 11:11:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.20_model.r WARNING @ Mon, 03 Jun 2019 11:11:52: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:11:52: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Mon, 03 Jun 2019 11:11:52: #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 11:11:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:11:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:11:55: 9000000 INFO @ Mon, 03 Jun 2019 11:12:06: 10000000 INFO @ Mon, 03 Jun 2019 11:12:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:12:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:12:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:12:14: #1 total tags in treatment: 10746131 INFO @ Mon, 03 Jun 2019 11:12:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:12:14: #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 11:12:14: #1 tags after filtering in treatment: 10746131 INFO @ Mon, 03 Jun 2019 11:12:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:12:14: #1 finished! INFO @ Mon, 03 Jun 2019 11:12:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:12:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:12:15: #2 number of paired peaks: 800 WARNING @ Mon, 03 Jun 2019 11:12:15: Fewer paired peaks (800) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 800 pairs to build model! INFO @ Mon, 03 Jun 2019 11:12:15: start model_add_line... INFO @ Mon, 03 Jun 2019 11:12:15: start X-correlation... INFO @ Mon, 03 Jun 2019 11:12:15: end of X-cor INFO @ Mon, 03 Jun 2019 11:12:15: #2 finished! INFO @ Mon, 03 Jun 2019 11:12:15: #2 predicted fragment length is 87 bps INFO @ Mon, 03 Jun 2019 11:12:15: #2 alternative fragment length(s) may be 87 bps INFO @ Mon, 03 Jun 2019 11:12:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.10_model.r WARNING @ Mon, 03 Jun 2019 11:12:15: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:12:15: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Mon, 03 Jun 2019 11:12:15: #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 11:12:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:12:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:12:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:12:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:12:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:12:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.05_summits.bed INFO @ Mon, 03 Jun 2019 11:12:28: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4667 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:12:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:12:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:12:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.20_summits.bed INFO @ Mon, 03 Jun 2019 11:12:39: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1123 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:12:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:13:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:13:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:13:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288014/SRX288014.10_summits.bed INFO @ Mon, 03 Jun 2019 11:13:03: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2159 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。