Job ID = 2590722 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,781,167 reads read : 57,562,334 reads written : 28,781,167 reads 0-length : 28,781,167 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:25 28781167 reads; of these: 28781167 (100.00%) were unpaired; of these: 675911 (2.35%) aligned 0 times 18639471 (64.76%) aligned exactly 1 time 9465785 (32.89%) aligned >1 times 97.65% overall alignment rate Time searching: 00:13:26 Overall time: 00:13:26 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] 10845513 / 28105256 = 0.3859 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 23:35:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.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 23:35:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:35:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:35:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.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 23:35:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:35:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:35:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.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 23:35:40: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:35:40: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:35:46: 1000000 INFO @ Mon, 12 Aug 2019 23:35:48: 1000000 INFO @ Mon, 12 Aug 2019 23:35:49: 1000000 INFO @ Mon, 12 Aug 2019 23:35:55: 2000000 INFO @ Mon, 12 Aug 2019 23:35:56: 2000000 INFO @ Mon, 12 Aug 2019 23:35:57: 2000000 INFO @ Mon, 12 Aug 2019 23:36:03: 3000000 INFO @ Mon, 12 Aug 2019 23:36:05: 3000000 INFO @ Mon, 12 Aug 2019 23:36:06: 3000000 INFO @ Mon, 12 Aug 2019 23:36:12: 4000000 INFO @ Mon, 12 Aug 2019 23:36:13: 4000000 INFO @ Mon, 12 Aug 2019 23:36:14: 4000000 INFO @ Mon, 12 Aug 2019 23:36:20: 5000000 INFO @ Mon, 12 Aug 2019 23:36:21: 5000000 INFO @ Mon, 12 Aug 2019 23:36:23: 5000000 INFO @ Mon, 12 Aug 2019 23:36:28: 6000000 INFO @ Mon, 12 Aug 2019 23:36:30: 6000000 INFO @ Mon, 12 Aug 2019 23:36:31: 6000000 INFO @ Mon, 12 Aug 2019 23:36:37: 7000000 INFO @ Mon, 12 Aug 2019 23:36:38: 7000000 INFO @ Mon, 12 Aug 2019 23:36:40: 7000000 INFO @ Mon, 12 Aug 2019 23:36:45: 8000000 INFO @ Mon, 12 Aug 2019 23:36:47: 8000000 INFO @ Mon, 12 Aug 2019 23:36:48: 8000000 INFO @ Mon, 12 Aug 2019 23:36:54: 9000000 INFO @ Mon, 12 Aug 2019 23:36:55: 9000000 INFO @ Mon, 12 Aug 2019 23:36:56: 9000000 INFO @ Mon, 12 Aug 2019 23:37:02: 10000000 INFO @ Mon, 12 Aug 2019 23:37:03: 10000000 INFO @ Mon, 12 Aug 2019 23:37:05: 10000000 INFO @ Mon, 12 Aug 2019 23:37:10: 11000000 INFO @ Mon, 12 Aug 2019 23:37:12: 11000000 INFO @ Mon, 12 Aug 2019 23:37:13: 11000000 INFO @ Mon, 12 Aug 2019 23:37:19: 12000000 INFO @ Mon, 12 Aug 2019 23:37:20: 12000000 INFO @ Mon, 12 Aug 2019 23:37:21: 12000000 INFO @ Mon, 12 Aug 2019 23:37:27: 13000000 INFO @ Mon, 12 Aug 2019 23:37:28: 13000000 INFO @ Mon, 12 Aug 2019 23:37:30: 13000000 INFO @ Mon, 12 Aug 2019 23:37:36: 14000000 INFO @ Mon, 12 Aug 2019 23:37:37: 14000000 INFO @ Mon, 12 Aug 2019 23:37:39: 14000000 INFO @ Mon, 12 Aug 2019 23:37:44: 15000000 INFO @ Mon, 12 Aug 2019 23:37:45: 15000000 INFO @ Mon, 12 Aug 2019 23:37:46: 15000000 INFO @ Mon, 12 Aug 2019 23:37:52: 16000000 INFO @ Mon, 12 Aug 2019 23:37:53: 16000000 INFO @ Mon, 12 Aug 2019 23:37:54: 16000000 INFO @ Mon, 12 Aug 2019 23:37:59: 17000000 INFO @ Mon, 12 Aug 2019 23:38:00: 17000000 INFO @ Mon, 12 Aug 2019 23:38:01: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:38:01: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:38:01: #1 total tags in treatment: 17259743 INFO @ Mon, 12 Aug 2019 23:38:01: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:38:01: #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 23:38:02: #1 tags after filtering in treatment: 17259743 INFO @ Mon, 12 Aug 2019 23:38:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:38:02: #1 finished! INFO @ Mon, 12 Aug 2019 23:38:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:38:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:38:02: 17000000 INFO @ Mon, 12 Aug 2019 23:38:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:38:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:38:03: #1 total tags in treatment: 17259743 INFO @ Mon, 12 Aug 2019 23:38:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:38:03: #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 23:38:03: #1 tags after filtering in treatment: 17259743 INFO @ Mon, 12 Aug 2019 23:38:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:38:03: #1 finished! INFO @ Mon, 12 Aug 2019 23:38:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:38:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:38:03: #2 number of paired peaks: 538 WARNING @ Mon, 12 Aug 2019 23:38:03: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Mon, 12 Aug 2019 23:38:03: start model_add_line... INFO @ Mon, 12 Aug 2019 23:38:03: start X-correlation... INFO @ Mon, 12 Aug 2019 23:38:03: end of X-cor INFO @ Mon, 12 Aug 2019 23:38:03: #2 finished! INFO @ Mon, 12 Aug 2019 23:38:03: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 23:38:03: #2 alternative fragment length(s) may be 4,53 bps INFO @ Mon, 12 Aug 2019 23:38:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.05_model.r WARNING @ Mon, 12 Aug 2019 23:38:03: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:38:03: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Mon, 12 Aug 2019 23:38:03: #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 23:38:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:38:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:38:04: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:38:04: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:38:04: #1 total tags in treatment: 17259743 INFO @ Mon, 12 Aug 2019 23:38:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:38:04: #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 23:38:04: #1 tags after filtering in treatment: 17259743 INFO @ Mon, 12 Aug 2019 23:38:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:38:04: #1 finished! INFO @ Mon, 12 Aug 2019 23:38:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:38:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:38:04: #2 number of paired peaks: 538 WARNING @ Mon, 12 Aug 2019 23:38:04: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Mon, 12 Aug 2019 23:38:04: start model_add_line... INFO @ Mon, 12 Aug 2019 23:38:05: start X-correlation... INFO @ Mon, 12 Aug 2019 23:38:05: end of X-cor INFO @ Mon, 12 Aug 2019 23:38:05: #2 finished! INFO @ Mon, 12 Aug 2019 23:38:05: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 23:38:05: #2 alternative fragment length(s) may be 4,53 bps INFO @ Mon, 12 Aug 2019 23:38:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.10_model.r WARNING @ Mon, 12 Aug 2019 23:38:05: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:38:05: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Mon, 12 Aug 2019 23:38:05: #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 23:38:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:38:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:38:06: #2 number of paired peaks: 538 WARNING @ Mon, 12 Aug 2019 23:38:06: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Mon, 12 Aug 2019 23:38:06: start model_add_line... INFO @ Mon, 12 Aug 2019 23:38:06: start X-correlation... INFO @ Mon, 12 Aug 2019 23:38:06: end of X-cor INFO @ Mon, 12 Aug 2019 23:38:06: #2 finished! INFO @ Mon, 12 Aug 2019 23:38:06: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 23:38:06: #2 alternative fragment length(s) may be 4,53 bps INFO @ Mon, 12 Aug 2019 23:38:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.20_model.r WARNING @ Mon, 12 Aug 2019 23:38:06: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:38:06: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Mon, 12 Aug 2019 23:38:06: #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 23:38:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:38:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:38:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:38:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:38:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:39:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:39:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:39:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.05_summits.bed INFO @ Mon, 12 Aug 2019 23:39:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3170 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:39:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:39:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:39:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.10_summits.bed INFO @ Mon, 12 Aug 2019 23:39:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2005 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:39:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:39:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:39:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011032/SRX5011032.20_summits.bed INFO @ Mon, 12 Aug 2019 23:39:13: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (1074 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。