Job ID = 1294988 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,667,108 reads read : 17,667,108 reads written : 17,667,108 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: 00:08:37 17667108 reads; of these: 17667108 (100.00%) were unpaired; of these: 720113 (4.08%) aligned 0 times 11489781 (65.03%) aligned exactly 1 time 5457214 (30.89%) aligned >1 times 95.92% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 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] 1984680 / 16946995 = 0.1171 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 11:25:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.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 11:25:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:25:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:25:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.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 11:25:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:25:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:25:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.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 11:25:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:25:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:26:04: 1000000 INFO @ Mon, 03 Jun 2019 11:26:06: 1000000 INFO @ Mon, 03 Jun 2019 11:26:06: 1000000 INFO @ Mon, 03 Jun 2019 11:26:12: 2000000 INFO @ Mon, 03 Jun 2019 11:26:15: 2000000 INFO @ Mon, 03 Jun 2019 11:26:16: 2000000 INFO @ Mon, 03 Jun 2019 11:26:19: 3000000 INFO @ Mon, 03 Jun 2019 11:26:23: 3000000 INFO @ Mon, 03 Jun 2019 11:26:25: 3000000 INFO @ Mon, 03 Jun 2019 11:26:26: 4000000 INFO @ Mon, 03 Jun 2019 11:26:32: 4000000 INFO @ Mon, 03 Jun 2019 11:26:34: 5000000 INFO @ Mon, 03 Jun 2019 11:26:34: 4000000 INFO @ Mon, 03 Jun 2019 11:26:40: 5000000 INFO @ Mon, 03 Jun 2019 11:26:41: 6000000 INFO @ Mon, 03 Jun 2019 11:26:43: 5000000 INFO @ Mon, 03 Jun 2019 11:26:48: 7000000 INFO @ Mon, 03 Jun 2019 11:26:49: 6000000 INFO @ Mon, 03 Jun 2019 11:26:52: 6000000 INFO @ Mon, 03 Jun 2019 11:26:56: 8000000 INFO @ Mon, 03 Jun 2019 11:26:57: 7000000 INFO @ Mon, 03 Jun 2019 11:27:01: 7000000 INFO @ Mon, 03 Jun 2019 11:27:03: 9000000 INFO @ Mon, 03 Jun 2019 11:27:06: 8000000 INFO @ Mon, 03 Jun 2019 11:27:10: 8000000 INFO @ Mon, 03 Jun 2019 11:27:11: 10000000 INFO @ Mon, 03 Jun 2019 11:27:14: 9000000 INFO @ Mon, 03 Jun 2019 11:27:18: 11000000 INFO @ Mon, 03 Jun 2019 11:27:19: 9000000 INFO @ Mon, 03 Jun 2019 11:27:23: 10000000 INFO @ Mon, 03 Jun 2019 11:27:26: 12000000 INFO @ Mon, 03 Jun 2019 11:27:27: 10000000 INFO @ Mon, 03 Jun 2019 11:27:31: 11000000 INFO @ Mon, 03 Jun 2019 11:27:33: 13000000 INFO @ Mon, 03 Jun 2019 11:27:36: 11000000 INFO @ Mon, 03 Jun 2019 11:27:40: 12000000 INFO @ Mon, 03 Jun 2019 11:27:40: 14000000 INFO @ Mon, 03 Jun 2019 11:27:45: 12000000 INFO @ Mon, 03 Jun 2019 11:27:48: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:27:48: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:27:48: #1 total tags in treatment: 14962315 INFO @ Mon, 03 Jun 2019 11:27:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:27:48: #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 11:27:48: #1 tags after filtering in treatment: 14962315 INFO @ Mon, 03 Jun 2019 11:27:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:27:48: #1 finished! INFO @ Mon, 03 Jun 2019 11:27:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:27:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:27:49: 13000000 INFO @ Mon, 03 Jun 2019 11:27:49: #2 number of paired peaks: 283 WARNING @ Mon, 03 Jun 2019 11:27:49: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Mon, 03 Jun 2019 11:27:49: start model_add_line... INFO @ Mon, 03 Jun 2019 11:27:49: start X-correlation... INFO @ Mon, 03 Jun 2019 11:27:49: end of X-cor INFO @ Mon, 03 Jun 2019 11:27:49: #2 finished! INFO @ Mon, 03 Jun 2019 11:27:49: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:27:49: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:27:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.05_model.r WARNING @ Mon, 03 Jun 2019 11:27:49: #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 11:27:49: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:27:49: #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 11:27:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:27:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:27:54: 13000000 INFO @ Mon, 03 Jun 2019 11:27:57: 14000000 INFO @ Mon, 03 Jun 2019 11:28:03: 14000000 INFO @ Mon, 03 Jun 2019 11:28:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:28:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:28:06: #1 total tags in treatment: 14962315 INFO @ Mon, 03 Jun 2019 11:28:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:28:06: #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 11:28:06: #1 tags after filtering in treatment: 14962315 INFO @ Mon, 03 Jun 2019 11:28:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:28:06: #1 finished! INFO @ Mon, 03 Jun 2019 11:28:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:28:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:28:07: #2 number of paired peaks: 283 WARNING @ Mon, 03 Jun 2019 11:28:07: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Mon, 03 Jun 2019 11:28:07: start model_add_line... INFO @ Mon, 03 Jun 2019 11:28:07: start X-correlation... INFO @ Mon, 03 Jun 2019 11:28:07: end of X-cor INFO @ Mon, 03 Jun 2019 11:28:07: #2 finished! INFO @ Mon, 03 Jun 2019 11:28:07: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:28:07: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:28:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.10_model.r WARNING @ Mon, 03 Jun 2019 11:28:07: #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 11:28:07: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:28:07: #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 11:28:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:28:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:28:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:28:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:28:12: #1 total tags in treatment: 14962315 INFO @ Mon, 03 Jun 2019 11:28:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:28:12: #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 11:28:12: #1 tags after filtering in treatment: 14962315 INFO @ Mon, 03 Jun 2019 11:28:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:28:12: #1 finished! INFO @ Mon, 03 Jun 2019 11:28:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:28:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:28:14: #2 number of paired peaks: 283 WARNING @ Mon, 03 Jun 2019 11:28:14: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Mon, 03 Jun 2019 11:28:14: start model_add_line... INFO @ Mon, 03 Jun 2019 11:28:14: start X-correlation... INFO @ Mon, 03 Jun 2019 11:28:14: end of X-cor INFO @ Mon, 03 Jun 2019 11:28:14: #2 finished! INFO @ Mon, 03 Jun 2019 11:28:14: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:28:14: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:28:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.20_model.r WARNING @ Mon, 03 Jun 2019 11:28:14: #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 11:28:14: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:28:14: #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 11:28:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:28:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:28:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:28:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:28:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:28:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:28:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.05_summits.bed INFO @ Mon, 03 Jun 2019 11:28:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2146 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:28:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:29:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:29:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:29:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.10_summits.bed INFO @ Mon, 03 Jun 2019 11:29:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1881 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:29:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:29:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:29:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288044/SRX288044.20_summits.bed INFO @ Mon, 03 Jun 2019 11:29:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1484 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。