Job ID = 1294882 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,133,552 reads read : 17,133,552 reads written : 17,133,552 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: 00:08:12 17133552 reads; of these: 17133552 (100.00%) were unpaired; of these: 669223 (3.91%) aligned 0 times 11145718 (65.05%) aligned exactly 1 time 5318611 (31.04%) aligned >1 times 96.09% overall alignment rate Time searching: 00:08:12 Overall time: 00:08:12 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] 2378408 / 16464329 = 0.1445 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 10:52:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.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 10:52:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:52:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:52:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.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 10:52:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:52:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:52:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.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 10:52:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:52:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:52:27: 1000000 INFO @ Mon, 03 Jun 2019 10:52:28: 1000000 INFO @ Mon, 03 Jun 2019 10:52:31: 1000000 INFO @ Mon, 03 Jun 2019 10:52:34: 2000000 INFO @ Mon, 03 Jun 2019 10:52:36: 2000000 INFO @ Mon, 03 Jun 2019 10:52:40: 2000000 INFO @ Mon, 03 Jun 2019 10:52:42: 3000000 INFO @ Mon, 03 Jun 2019 10:52:44: 3000000 INFO @ Mon, 03 Jun 2019 10:52:49: 4000000 INFO @ Mon, 03 Jun 2019 10:52:51: 3000000 INFO @ Mon, 03 Jun 2019 10:52:51: 4000000 INFO @ Mon, 03 Jun 2019 10:52:56: 5000000 INFO @ Mon, 03 Jun 2019 10:52:59: 5000000 INFO @ Mon, 03 Jun 2019 10:53:00: 4000000 INFO @ Mon, 03 Jun 2019 10:53:03: 6000000 INFO @ Mon, 03 Jun 2019 10:53:06: 6000000 INFO @ Mon, 03 Jun 2019 10:53:10: 5000000 INFO @ Mon, 03 Jun 2019 10:53:10: 7000000 INFO @ Mon, 03 Jun 2019 10:53:14: 7000000 INFO @ Mon, 03 Jun 2019 10:53:17: 8000000 INFO @ Mon, 03 Jun 2019 10:53:19: 6000000 INFO @ Mon, 03 Jun 2019 10:53:21: 8000000 INFO @ Mon, 03 Jun 2019 10:53:23: 9000000 INFO @ Mon, 03 Jun 2019 10:53:28: 7000000 INFO @ Mon, 03 Jun 2019 10:53:29: 9000000 INFO @ Mon, 03 Jun 2019 10:53:30: 10000000 INFO @ Mon, 03 Jun 2019 10:53:36: 10000000 INFO @ Mon, 03 Jun 2019 10:53:37: 8000000 INFO @ Mon, 03 Jun 2019 10:53:38: 11000000 INFO @ Mon, 03 Jun 2019 10:53:44: 11000000 INFO @ Mon, 03 Jun 2019 10:53:45: 12000000 INFO @ Mon, 03 Jun 2019 10:53:47: 9000000 INFO @ Mon, 03 Jun 2019 10:53:52: 12000000 INFO @ Mon, 03 Jun 2019 10:53:52: 13000000 INFO @ Mon, 03 Jun 2019 10:53:57: 10000000 INFO @ Mon, 03 Jun 2019 10:53:59: 14000000 INFO @ Mon, 03 Jun 2019 10:53:59: 13000000 INFO @ Mon, 03 Jun 2019 10:54:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:54:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:54:00: #1 total tags in treatment: 14085921 INFO @ Mon, 03 Jun 2019 10:54:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:54:00: #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 10:54:00: #1 tags after filtering in treatment: 14085921 INFO @ Mon, 03 Jun 2019 10:54:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:54:00: #1 finished! INFO @ Mon, 03 Jun 2019 10:54:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:54:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:54:01: #2 number of paired peaks: 348 WARNING @ Mon, 03 Jun 2019 10:54:01: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Mon, 03 Jun 2019 10:54:01: start model_add_line... INFO @ Mon, 03 Jun 2019 10:54:02: start X-correlation... INFO @ Mon, 03 Jun 2019 10:54:02: end of X-cor INFO @ Mon, 03 Jun 2019 10:54:02: #2 finished! INFO @ Mon, 03 Jun 2019 10:54:02: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:54:02: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:54:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.05_model.r WARNING @ Mon, 03 Jun 2019 10:54:02: #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 10:54:02: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:54:02: #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 10:54:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:54:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:54:07: 11000000 INFO @ Mon, 03 Jun 2019 10:54:07: 14000000 INFO @ Mon, 03 Jun 2019 10:54:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:54:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:54:08: #1 total tags in treatment: 14085921 INFO @ Mon, 03 Jun 2019 10:54:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:54:08: #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 10:54:08: #1 tags after filtering in treatment: 14085921 INFO @ Mon, 03 Jun 2019 10:54:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:54:08: #1 finished! INFO @ Mon, 03 Jun 2019 10:54:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:54:09: #2 number of paired peaks: 348 WARNING @ Mon, 03 Jun 2019 10:54:09: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Mon, 03 Jun 2019 10:54:09: start model_add_line... INFO @ Mon, 03 Jun 2019 10:54:09: start X-correlation... INFO @ Mon, 03 Jun 2019 10:54:09: end of X-cor INFO @ Mon, 03 Jun 2019 10:54:09: #2 finished! INFO @ Mon, 03 Jun 2019 10:54:09: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:54:09: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:54:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.10_model.r WARNING @ Mon, 03 Jun 2019 10:54:09: #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 10:54:09: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:54:09: #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 10:54:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:54:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:54:16: 12000000 INFO @ Mon, 03 Jun 2019 10:54:26: 13000000 INFO @ Mon, 03 Jun 2019 10:54:35: 14000000 INFO @ Mon, 03 Jun 2019 10:54:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:54:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:54:36: #1 total tags in treatment: 14085921 INFO @ Mon, 03 Jun 2019 10:54:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:54:36: #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 10:54:36: #1 tags after filtering in treatment: 14085921 INFO @ Mon, 03 Jun 2019 10:54:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:54:36: #1 finished! INFO @ Mon, 03 Jun 2019 10:54:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:54:37: #2 number of paired peaks: 348 WARNING @ Mon, 03 Jun 2019 10:54:37: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Mon, 03 Jun 2019 10:54:37: start model_add_line... INFO @ Mon, 03 Jun 2019 10:54:37: start X-correlation... INFO @ Mon, 03 Jun 2019 10:54:37: end of X-cor INFO @ Mon, 03 Jun 2019 10:54:37: #2 finished! INFO @ Mon, 03 Jun 2019 10:54:37: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:54:37: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:54:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.20_model.r WARNING @ Mon, 03 Jun 2019 10:54:37: #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 10:54:37: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:54:37: #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 10:54:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:54:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:54:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:54:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:54:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:54:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:54:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.05_summits.bed INFO @ Mon, 03 Jun 2019 10:54:58: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2162 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:55:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:55:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:55:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.10_summits.bed INFO @ Mon, 03 Jun 2019 10:55:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1913 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:55:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:55:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:55:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:55:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287960/SRX287960.20_summits.bed INFO @ Mon, 03 Jun 2019 10:55:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1492 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。