Job ID = 1293322 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,164,099 reads read : 26,164,099 reads written : 26,164,099 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:38 26164099 reads; of these: 26164099 (100.00%) were unpaired; of these: 5531698 (21.14%) aligned 0 times 19556809 (74.75%) aligned exactly 1 time 1075592 (4.11%) aligned >1 times 78.86% overall alignment rate Time searching: 00:07:39 Overall time: 00:07:39 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] 10290389 / 20632401 = 0.4987 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 @ Sun, 02 Jun 2019 23:27:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.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 @ Sun, 02 Jun 2019 23:27:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:27:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:27:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.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 @ Sun, 02 Jun 2019 23:27:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:27:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:27:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.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 @ Sun, 02 Jun 2019 23:27:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:27:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:27:18: 1000000 INFO @ Sun, 02 Jun 2019 23:27:20: 1000000 INFO @ Sun, 02 Jun 2019 23:27:21: 1000000 INFO @ Sun, 02 Jun 2019 23:27:27: 2000000 INFO @ Sun, 02 Jun 2019 23:27:30: 2000000 INFO @ Sun, 02 Jun 2019 23:27:32: 2000000 INFO @ Sun, 02 Jun 2019 23:27:36: 3000000 INFO @ Sun, 02 Jun 2019 23:27:41: 3000000 INFO @ Sun, 02 Jun 2019 23:27:44: 3000000 INFO @ Sun, 02 Jun 2019 23:27:44: 4000000 INFO @ Sun, 02 Jun 2019 23:27:52: 4000000 INFO @ Sun, 02 Jun 2019 23:27:53: 5000000 INFO @ Sun, 02 Jun 2019 23:27:56: 4000000 INFO @ Sun, 02 Jun 2019 23:28:02: 6000000 INFO @ Sun, 02 Jun 2019 23:28:03: 5000000 INFO @ Sun, 02 Jun 2019 23:28:08: 5000000 INFO @ Sun, 02 Jun 2019 23:28:10: 7000000 INFO @ Sun, 02 Jun 2019 23:28:13: 6000000 INFO @ Sun, 02 Jun 2019 23:28:19: 6000000 INFO @ Sun, 02 Jun 2019 23:28:19: 8000000 INFO @ Sun, 02 Jun 2019 23:28:23: 7000000 INFO @ Sun, 02 Jun 2019 23:28:28: 9000000 INFO @ Sun, 02 Jun 2019 23:28:30: 7000000 INFO @ Sun, 02 Jun 2019 23:28:33: 8000000 INFO @ Sun, 02 Jun 2019 23:28:36: 10000000 INFO @ Sun, 02 Jun 2019 23:28:39: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 23:28:39: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 23:28:39: #1 total tags in treatment: 10342012 INFO @ Sun, 02 Jun 2019 23:28:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:28:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:28:40: #1 tags after filtering in treatment: 10342012 INFO @ Sun, 02 Jun 2019 23:28:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:28:40: #1 finished! INFO @ Sun, 02 Jun 2019 23:28:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:28:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:28:41: #2 number of paired peaks: 7185 INFO @ Sun, 02 Jun 2019 23:28:41: start model_add_line... INFO @ Sun, 02 Jun 2019 23:28:41: start X-correlation... INFO @ Sun, 02 Jun 2019 23:28:42: end of X-cor INFO @ Sun, 02 Jun 2019 23:28:42: #2 finished! INFO @ Sun, 02 Jun 2019 23:28:42: #2 predicted fragment length is 100 bps INFO @ Sun, 02 Jun 2019 23:28:42: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 02 Jun 2019 23:28:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.05_model.r WARNING @ Sun, 02 Jun 2019 23:28:42: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:28:42: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sun, 02 Jun 2019 23:28:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:28:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:28:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:28:42: 8000000 INFO @ Sun, 02 Jun 2019 23:28:43: 9000000 INFO @ Sun, 02 Jun 2019 23:28:53: 10000000 INFO @ Sun, 02 Jun 2019 23:28:53: 9000000 INFO @ Sun, 02 Jun 2019 23:28:56: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 23:28:56: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 23:28:56: #1 total tags in treatment: 10342012 INFO @ Sun, 02 Jun 2019 23:28:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:28:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:28:57: #1 tags after filtering in treatment: 10342012 INFO @ Sun, 02 Jun 2019 23:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:28:57: #1 finished! INFO @ Sun, 02 Jun 2019 23:28:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:28:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:28:58: #2 number of paired peaks: 7185 INFO @ Sun, 02 Jun 2019 23:28:58: start model_add_line... INFO @ Sun, 02 Jun 2019 23:28:58: start X-correlation... INFO @ Sun, 02 Jun 2019 23:28:58: end of X-cor INFO @ Sun, 02 Jun 2019 23:28:58: #2 finished! INFO @ Sun, 02 Jun 2019 23:28:58: #2 predicted fragment length is 100 bps INFO @ Sun, 02 Jun 2019 23:28:58: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 02 Jun 2019 23:28:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.10_model.r WARNING @ Sun, 02 Jun 2019 23:28:58: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:28:58: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sun, 02 Jun 2019 23:28:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:28:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:28:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:29:04: 10000000 INFO @ Sun, 02 Jun 2019 23:29:08: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 23:29:08: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 23:29:08: #1 total tags in treatment: 10342012 INFO @ Sun, 02 Jun 2019 23:29:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:29:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:29:08: #1 tags after filtering in treatment: 10342012 INFO @ Sun, 02 Jun 2019 23:29:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:29:08: #1 finished! INFO @ Sun, 02 Jun 2019 23:29:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:29:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:29:10: #2 number of paired peaks: 7185 INFO @ Sun, 02 Jun 2019 23:29:10: start model_add_line... INFO @ Sun, 02 Jun 2019 23:29:10: start X-correlation... INFO @ Sun, 02 Jun 2019 23:29:10: end of X-cor INFO @ Sun, 02 Jun 2019 23:29:10: #2 finished! INFO @ Sun, 02 Jun 2019 23:29:10: #2 predicted fragment length is 100 bps INFO @ Sun, 02 Jun 2019 23:29:10: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 02 Jun 2019 23:29:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.20_model.r WARNING @ Sun, 02 Jun 2019 23:29:10: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:29:10: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sun, 02 Jun 2019 23:29:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:29:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:29:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:29:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:29:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:29:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:29:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.05_summits.bed INFO @ Sun, 02 Jun 2019 23:29:31: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (12778 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:29:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:29:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:29:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:29:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:29:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.10_summits.bed INFO @ Sun, 02 Jun 2019 23:29:48: Done! pass1 - making usageList (13 chroms): 5 millis pass2 - checking and writing primary data (10003 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:29:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:29:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:29:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX102373/ERX102373.20_summits.bed INFO @ Sun, 02 Jun 2019 23:29:58: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7495 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。