Job ID = 2590312 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,098,275 reads read : 23,098,275 reads written : 23,098,275 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: 00:09:06 23098275 reads; of these: 23098275 (100.00%) were unpaired; of these: 3263405 (14.13%) aligned 0 times 12403291 (53.70%) aligned exactly 1 time 7431579 (32.17%) aligned >1 times 85.87% overall alignment rate Time searching: 00:09:06 Overall time: 00:09:06 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] 2631265 / 19834870 = 0.1327 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 21:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.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 21:03:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:03:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:03:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.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 21:03:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:03:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:03:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.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 21:03:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:03:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:03:36: 1000000 INFO @ Mon, 12 Aug 2019 21:03:36: 1000000 INFO @ Mon, 12 Aug 2019 21:03:37: 1000000 INFO @ Mon, 12 Aug 2019 21:03:44: 2000000 INFO @ Mon, 12 Aug 2019 21:03:47: 2000000 INFO @ Mon, 12 Aug 2019 21:03:48: 2000000 INFO @ Mon, 12 Aug 2019 21:03:52: 3000000 INFO @ Mon, 12 Aug 2019 21:03:58: 3000000 INFO @ Mon, 12 Aug 2019 21:03:59: 3000000 INFO @ Mon, 12 Aug 2019 21:04:00: 4000000 INFO @ Mon, 12 Aug 2019 21:04:08: 5000000 INFO @ Mon, 12 Aug 2019 21:04:08: 4000000 INFO @ Mon, 12 Aug 2019 21:04:09: 4000000 INFO @ Mon, 12 Aug 2019 21:04:15: 6000000 INFO @ Mon, 12 Aug 2019 21:04:18: 5000000 INFO @ Mon, 12 Aug 2019 21:04:19: 5000000 INFO @ Mon, 12 Aug 2019 21:04:23: 7000000 INFO @ Mon, 12 Aug 2019 21:04:28: 6000000 INFO @ Mon, 12 Aug 2019 21:04:29: 6000000 INFO @ Mon, 12 Aug 2019 21:04:31: 8000000 INFO @ Mon, 12 Aug 2019 21:04:37: 7000000 INFO @ Mon, 12 Aug 2019 21:04:38: 7000000 INFO @ Mon, 12 Aug 2019 21:04:38: 9000000 INFO @ Mon, 12 Aug 2019 21:04:46: 8000000 INFO @ Mon, 12 Aug 2019 21:04:46: 10000000 INFO @ Mon, 12 Aug 2019 21:04:47: 8000000 INFO @ Mon, 12 Aug 2019 21:04:54: 11000000 INFO @ Mon, 12 Aug 2019 21:04:55: 9000000 INFO @ Mon, 12 Aug 2019 21:04:56: 9000000 INFO @ Mon, 12 Aug 2019 21:05:02: 12000000 INFO @ Mon, 12 Aug 2019 21:05:04: 10000000 INFO @ Mon, 12 Aug 2019 21:05:05: 10000000 INFO @ Mon, 12 Aug 2019 21:05:10: 13000000 INFO @ Mon, 12 Aug 2019 21:05:13: 11000000 INFO @ Mon, 12 Aug 2019 21:05:14: 11000000 INFO @ Mon, 12 Aug 2019 21:05:18: 14000000 INFO @ Mon, 12 Aug 2019 21:05:23: 12000000 INFO @ Mon, 12 Aug 2019 21:05:23: 12000000 INFO @ Mon, 12 Aug 2019 21:05:25: 15000000 INFO @ Mon, 12 Aug 2019 21:05:32: 13000000 INFO @ Mon, 12 Aug 2019 21:05:32: 13000000 INFO @ Mon, 12 Aug 2019 21:05:33: 16000000 INFO @ Mon, 12 Aug 2019 21:05:40: 14000000 INFO @ Mon, 12 Aug 2019 21:05:41: 14000000 INFO @ Mon, 12 Aug 2019 21:05:41: 17000000 INFO @ Mon, 12 Aug 2019 21:05:43: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:05:43: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:05:43: #1 total tags in treatment: 17203605 INFO @ Mon, 12 Aug 2019 21:05:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:05:43: #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 21:05:43: #1 tags after filtering in treatment: 17203605 INFO @ Mon, 12 Aug 2019 21:05:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:05:43: #1 finished! INFO @ Mon, 12 Aug 2019 21:05:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:05:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:05:44: #2 number of paired peaks: 410 WARNING @ Mon, 12 Aug 2019 21:05:44: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Mon, 12 Aug 2019 21:05:44: start model_add_line... INFO @ Mon, 12 Aug 2019 21:05:45: start X-correlation... INFO @ Mon, 12 Aug 2019 21:05:45: end of X-cor INFO @ Mon, 12 Aug 2019 21:05:45: #2 finished! INFO @ Mon, 12 Aug 2019 21:05:45: #2 predicted fragment length is 54 bps INFO @ Mon, 12 Aug 2019 21:05:45: #2 alternative fragment length(s) may be 2,54,558 bps INFO @ Mon, 12 Aug 2019 21:05:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.20_model.r WARNING @ Mon, 12 Aug 2019 21:05:45: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:05:45: #2 You may need to consider one of the other alternative d(s): 2,54,558 WARNING @ Mon, 12 Aug 2019 21:05:45: #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 21:05:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:05:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:05:50: 15000000 INFO @ Mon, 12 Aug 2019 21:05:50: 15000000 INFO @ Mon, 12 Aug 2019 21:05:59: 16000000 INFO @ Mon, 12 Aug 2019 21:05:59: 16000000 INFO @ Mon, 12 Aug 2019 21:06:08: 17000000 INFO @ Mon, 12 Aug 2019 21:06:08: 17000000 INFO @ Mon, 12 Aug 2019 21:06:10: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:06:10: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:06:10: #1 total tags in treatment: 17203605 INFO @ Mon, 12 Aug 2019 21:06:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:06:10: #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 21:06:10: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:06:10: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:06:10: #1 total tags in treatment: 17203605 INFO @ Mon, 12 Aug 2019 21:06:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:06:10: #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 21:06:10: #1 tags after filtering in treatment: 17203605 INFO @ Mon, 12 Aug 2019 21:06:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:06:10: #1 finished! INFO @ Mon, 12 Aug 2019 21:06:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:06:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:06:11: #1 tags after filtering in treatment: 17203605 INFO @ Mon, 12 Aug 2019 21:06:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:06:11: #1 finished! INFO @ Mon, 12 Aug 2019 21:06:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:06:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:06:12: #2 number of paired peaks: 410 WARNING @ Mon, 12 Aug 2019 21:06:12: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Mon, 12 Aug 2019 21:06:12: start model_add_line... INFO @ Mon, 12 Aug 2019 21:06:12: start X-correlation... INFO @ Mon, 12 Aug 2019 21:06:12: end of X-cor INFO @ Mon, 12 Aug 2019 21:06:12: #2 finished! INFO @ Mon, 12 Aug 2019 21:06:12: #2 predicted fragment length is 54 bps INFO @ Mon, 12 Aug 2019 21:06:12: #2 alternative fragment length(s) may be 2,54,558 bps INFO @ Mon, 12 Aug 2019 21:06:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.05_model.r WARNING @ Mon, 12 Aug 2019 21:06:12: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:06:12: #2 You may need to consider one of the other alternative d(s): 2,54,558 WARNING @ Mon, 12 Aug 2019 21:06:12: #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 21:06:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:06:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:06:12: #2 number of paired peaks: 410 WARNING @ Mon, 12 Aug 2019 21:06:12: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Mon, 12 Aug 2019 21:06:12: start model_add_line... INFO @ Mon, 12 Aug 2019 21:06:12: start X-correlation... INFO @ Mon, 12 Aug 2019 21:06:12: end of X-cor INFO @ Mon, 12 Aug 2019 21:06:12: #2 finished! INFO @ Mon, 12 Aug 2019 21:06:12: #2 predicted fragment length is 54 bps INFO @ Mon, 12 Aug 2019 21:06:12: #2 alternative fragment length(s) may be 2,54,558 bps INFO @ Mon, 12 Aug 2019 21:06:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.10_model.r WARNING @ Mon, 12 Aug 2019 21:06:12: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:06:12: #2 You may need to consider one of the other alternative d(s): 2,54,558 WARNING @ Mon, 12 Aug 2019 21:06:12: #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 21:06:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:06:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:06:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:06:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:06:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:06:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.20_summits.bed INFO @ Mon, 12 Aug 2019 21:06:51: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (531 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:06:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:06:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:07:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:07:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:07:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.05_summits.bed INFO @ Mon, 12 Aug 2019 21:07:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2767 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:07:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:07:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331418/SRX331418.10_summits.bed INFO @ Mon, 12 Aug 2019 21:07:19: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1366 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。