Job ID = 2590665 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,240,584 reads read : 46,481,168 reads written : 23,240,584 reads 0-length : 23,240,584 rm: cannot remove ‘[DSE]RR*’: 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: 00:09:27 23240584 reads; of these: 23240584 (100.00%) were unpaired; of these: 489479 (2.11%) aligned 0 times 16151142 (69.50%) aligned exactly 1 time 6599963 (28.40%) aligned >1 times 97.89% overall alignment rate Time searching: 00:09:27 Overall time: 00:09:27 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] 8969982 / 22751105 = 0.3943 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, 12 Aug 2019 23:18:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.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, 12 Aug 2019 23:18:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:18:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:18:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.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, 12 Aug 2019 23:18:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:18:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:18:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.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, 12 Aug 2019 23:18:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:18:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:18:11: 1000000 INFO @ Mon, 12 Aug 2019 23:18:11: 1000000 INFO @ Mon, 12 Aug 2019 23:18:13: 1000000 INFO @ Mon, 12 Aug 2019 23:18:20: 2000000 INFO @ Mon, 12 Aug 2019 23:18:20: 2000000 INFO @ Mon, 12 Aug 2019 23:18:22: 2000000 INFO @ Mon, 12 Aug 2019 23:18:28: 3000000 INFO @ Mon, 12 Aug 2019 23:18:29: 3000000 INFO @ Mon, 12 Aug 2019 23:18:31: 3000000 INFO @ Mon, 12 Aug 2019 23:18:37: 4000000 INFO @ Mon, 12 Aug 2019 23:18:38: 4000000 INFO @ Mon, 12 Aug 2019 23:18:40: 4000000 INFO @ Mon, 12 Aug 2019 23:18:45: 5000000 INFO @ Mon, 12 Aug 2019 23:18:47: 5000000 INFO @ Mon, 12 Aug 2019 23:18:49: 5000000 INFO @ Mon, 12 Aug 2019 23:18:54: 6000000 INFO @ Mon, 12 Aug 2019 23:18:56: 6000000 INFO @ Mon, 12 Aug 2019 23:18:58: 6000000 INFO @ Mon, 12 Aug 2019 23:19:02: 7000000 INFO @ Mon, 12 Aug 2019 23:19:05: 7000000 INFO @ Mon, 12 Aug 2019 23:19:07: 7000000 INFO @ Mon, 12 Aug 2019 23:19:13: 8000000 INFO @ Mon, 12 Aug 2019 23:19:16: 8000000 INFO @ Mon, 12 Aug 2019 23:19:16: 8000000 INFO @ Mon, 12 Aug 2019 23:19:23: 9000000 INFO @ Mon, 12 Aug 2019 23:19:25: 9000000 INFO @ Mon, 12 Aug 2019 23:19:27: 9000000 INFO @ Mon, 12 Aug 2019 23:19:33: 10000000 INFO @ Mon, 12 Aug 2019 23:19:34: 10000000 INFO @ Mon, 12 Aug 2019 23:19:37: 10000000 INFO @ Mon, 12 Aug 2019 23:19:42: 11000000 INFO @ Mon, 12 Aug 2019 23:19:44: 11000000 INFO @ Mon, 12 Aug 2019 23:19:47: 11000000 INFO @ Mon, 12 Aug 2019 23:19:52: 12000000 INFO @ Mon, 12 Aug 2019 23:19:52: 12000000 INFO @ Mon, 12 Aug 2019 23:19:56: 12000000 INFO @ Mon, 12 Aug 2019 23:20:01: 13000000 INFO @ Mon, 12 Aug 2019 23:20:02: 13000000 INFO @ Mon, 12 Aug 2019 23:20:06: 13000000 INFO @ Mon, 12 Aug 2019 23:20:07: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:20:07: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:20:07: #1 total tags in treatment: 13781123 INFO @ Mon, 12 Aug 2019 23:20:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:20:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:20:08: #1 tags after filtering in treatment: 13781123 INFO @ Mon, 12 Aug 2019 23:20:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:20:08: #1 finished! INFO @ Mon, 12 Aug 2019 23:20:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:20:09: #2 number of paired peaks: 480 WARNING @ Mon, 12 Aug 2019 23:20:09: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Mon, 12 Aug 2019 23:20:09: start model_add_line... INFO @ Mon, 12 Aug 2019 23:20:09: start X-correlation... INFO @ Mon, 12 Aug 2019 23:20:09: end of X-cor INFO @ Mon, 12 Aug 2019 23:20:09: #2 finished! INFO @ Mon, 12 Aug 2019 23:20:09: #2 predicted fragment length is 59 bps INFO @ Mon, 12 Aug 2019 23:20:09: #2 alternative fragment length(s) may be 4,59 bps INFO @ Mon, 12 Aug 2019 23:20:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.20_model.r WARNING @ Mon, 12 Aug 2019 23:20:09: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:20:09: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Mon, 12 Aug 2019 23:20:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:20:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:20:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:20:09: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:20:09: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:20:09: #1 total tags in treatment: 13781123 INFO @ Mon, 12 Aug 2019 23:20:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:20:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:20:10: #1 tags after filtering in treatment: 13781123 INFO @ Mon, 12 Aug 2019 23:20:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:20:10: #1 finished! INFO @ Mon, 12 Aug 2019 23:20:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:20:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:20:11: #2 number of paired peaks: 480 WARNING @ Mon, 12 Aug 2019 23:20:11: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Mon, 12 Aug 2019 23:20:11: start model_add_line... INFO @ Mon, 12 Aug 2019 23:20:11: start X-correlation... INFO @ Mon, 12 Aug 2019 23:20:11: end of X-cor INFO @ Mon, 12 Aug 2019 23:20:11: #2 finished! INFO @ Mon, 12 Aug 2019 23:20:11: #2 predicted fragment length is 59 bps INFO @ Mon, 12 Aug 2019 23:20:11: #2 alternative fragment length(s) may be 4,59 bps INFO @ Mon, 12 Aug 2019 23:20:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.10_model.r WARNING @ Mon, 12 Aug 2019 23:20:11: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:20:11: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Mon, 12 Aug 2019 23:20:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:20:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:20:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:20:14: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:20:14: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:20:14: #1 total tags in treatment: 13781123 INFO @ Mon, 12 Aug 2019 23:20:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:20:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:20:14: #1 tags after filtering in treatment: 13781123 INFO @ Mon, 12 Aug 2019 23:20:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:20:14: #1 finished! INFO @ Mon, 12 Aug 2019 23:20:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:20:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:20:15: #2 number of paired peaks: 480 WARNING @ Mon, 12 Aug 2019 23:20:15: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Mon, 12 Aug 2019 23:20:15: start model_add_line... INFO @ Mon, 12 Aug 2019 23:20:15: start X-correlation... INFO @ Mon, 12 Aug 2019 23:20:15: end of X-cor INFO @ Mon, 12 Aug 2019 23:20:15: #2 finished! INFO @ Mon, 12 Aug 2019 23:20:15: #2 predicted fragment length is 59 bps INFO @ Mon, 12 Aug 2019 23:20:15: #2 alternative fragment length(s) may be 4,59 bps INFO @ Mon, 12 Aug 2019 23:20:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.05_model.r WARNING @ Mon, 12 Aug 2019 23:20:15: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:20:15: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Mon, 12 Aug 2019 23:20:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:20:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:20:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:20:47: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:20:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:20:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:21:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:21:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:21:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.20_summits.bed INFO @ Mon, 12 Aug 2019 23:21:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (801 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:21:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:21:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:21:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.10_summits.bed INFO @ Mon, 12 Aug 2019 23:21:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1650 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011014/SRX5011014.05_summits.bed INFO @ Mon, 12 Aug 2019 23:21:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2993 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。