Job ID = 2590799 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 39,285,389 reads read : 78,570,778 reads written : 39,285,389 reads 0-length : 39,285,389 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: 00:17:38 39285389 reads; of these: 39285389 (100.00%) were unpaired; of these: 821568 (2.09%) aligned 0 times 26305865 (66.96%) aligned exactly 1 time 12157956 (30.95%) aligned >1 times 97.91% overall alignment rate Time searching: 00:17:38 Overall time: 00:17:38 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 16 files... [bam_rmdupse_core] 13902821 / 38463821 = 0.3615 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 23:48:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.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 23:48:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:48:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:48:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.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 23:48:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:48:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:48:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.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 23:48:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:48:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:48:49: 1000000 INFO @ Mon, 12 Aug 2019 23:48:52: 1000000 INFO @ Mon, 12 Aug 2019 23:48:53: 1000000 INFO @ Mon, 12 Aug 2019 23:48:58: 2000000 INFO @ Mon, 12 Aug 2019 23:48:59: 2000000 INFO @ Mon, 12 Aug 2019 23:49:01: 2000000 INFO @ Mon, 12 Aug 2019 23:49:07: 3000000 INFO @ Mon, 12 Aug 2019 23:49:08: 3000000 INFO @ Mon, 12 Aug 2019 23:49:10: 3000000 INFO @ Mon, 12 Aug 2019 23:49:16: 4000000 INFO @ Mon, 12 Aug 2019 23:49:16: 4000000 INFO @ Mon, 12 Aug 2019 23:49:18: 4000000 INFO @ Mon, 12 Aug 2019 23:49:23: 5000000 INFO @ Mon, 12 Aug 2019 23:49:26: 5000000 INFO @ Mon, 12 Aug 2019 23:49:26: 5000000 INFO @ Mon, 12 Aug 2019 23:49:30: 6000000 INFO @ Mon, 12 Aug 2019 23:49:35: 6000000 INFO @ Mon, 12 Aug 2019 23:49:36: 6000000 INFO @ Mon, 12 Aug 2019 23:49:37: 7000000 INFO @ Mon, 12 Aug 2019 23:49:43: 7000000 INFO @ Mon, 12 Aug 2019 23:49:44: 8000000 INFO @ Mon, 12 Aug 2019 23:49:46: 7000000 INFO @ Mon, 12 Aug 2019 23:49:51: 8000000 INFO @ Mon, 12 Aug 2019 23:49:51: 9000000 INFO @ Mon, 12 Aug 2019 23:49:55: 8000000 INFO @ Mon, 12 Aug 2019 23:49:58: 10000000 INFO @ Mon, 12 Aug 2019 23:49:59: 9000000 INFO @ Mon, 12 Aug 2019 23:50:04: 9000000 INFO @ Mon, 12 Aug 2019 23:50:05: 11000000 INFO @ Mon, 12 Aug 2019 23:50:07: 10000000 INFO @ Mon, 12 Aug 2019 23:50:12: 12000000 INFO @ Mon, 12 Aug 2019 23:50:13: 10000000 INFO @ Mon, 12 Aug 2019 23:50:14: 11000000 INFO @ Mon, 12 Aug 2019 23:50:19: 13000000 INFO @ Mon, 12 Aug 2019 23:50:22: 12000000 INFO @ Mon, 12 Aug 2019 23:50:22: 11000000 INFO @ Mon, 12 Aug 2019 23:50:26: 14000000 INFO @ Mon, 12 Aug 2019 23:50:30: 13000000 INFO @ Mon, 12 Aug 2019 23:50:31: 12000000 INFO @ Mon, 12 Aug 2019 23:50:33: 15000000 INFO @ Mon, 12 Aug 2019 23:50:38: 14000000 INFO @ Mon, 12 Aug 2019 23:50:40: 16000000 INFO @ Mon, 12 Aug 2019 23:50:41: 13000000 INFO @ Mon, 12 Aug 2019 23:50:45: 15000000 INFO @ Mon, 12 Aug 2019 23:50:47: 17000000 INFO @ Mon, 12 Aug 2019 23:50:50: 14000000 INFO @ Mon, 12 Aug 2019 23:50:53: 16000000 INFO @ Mon, 12 Aug 2019 23:50:54: 18000000 INFO @ Mon, 12 Aug 2019 23:50:59: 15000000 INFO @ Mon, 12 Aug 2019 23:51:01: 17000000 INFO @ Mon, 12 Aug 2019 23:51:01: 19000000 INFO @ Mon, 12 Aug 2019 23:51:08: 16000000 INFO @ Mon, 12 Aug 2019 23:51:08: 20000000 INFO @ Mon, 12 Aug 2019 23:51:09: 18000000 INFO @ Mon, 12 Aug 2019 23:51:15: 21000000 INFO @ Mon, 12 Aug 2019 23:51:17: 19000000 INFO @ Mon, 12 Aug 2019 23:51:17: 17000000 INFO @ Mon, 12 Aug 2019 23:51:22: 22000000 INFO @ Mon, 12 Aug 2019 23:51:24: 20000000 INFO @ Mon, 12 Aug 2019 23:51:26: 18000000 INFO @ Mon, 12 Aug 2019 23:51:29: 23000000 INFO @ Mon, 12 Aug 2019 23:51:32: 21000000 INFO @ Mon, 12 Aug 2019 23:51:35: 19000000 INFO @ Mon, 12 Aug 2019 23:51:36: 24000000 INFO @ Mon, 12 Aug 2019 23:51:40: 22000000 INFO @ Mon, 12 Aug 2019 23:51:40: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:51:40: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:51:40: #1 total tags in treatment: 24561000 INFO @ Mon, 12 Aug 2019 23:51:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:51:40: #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 23:51:41: #1 tags after filtering in treatment: 24561000 INFO @ Mon, 12 Aug 2019 23:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:51:41: #1 finished! INFO @ Mon, 12 Aug 2019 23:51:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:51:43: #2 number of paired peaks: 311 WARNING @ Mon, 12 Aug 2019 23:51:43: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Mon, 12 Aug 2019 23:51:43: start model_add_line... INFO @ Mon, 12 Aug 2019 23:51:43: start X-correlation... INFO @ Mon, 12 Aug 2019 23:51:43: end of X-cor INFO @ Mon, 12 Aug 2019 23:51:43: #2 finished! INFO @ Mon, 12 Aug 2019 23:51:43: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 23:51:43: #2 alternative fragment length(s) may be 3,47 bps INFO @ Mon, 12 Aug 2019 23:51:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.10_model.r WARNING @ Mon, 12 Aug 2019 23:51:43: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:51:43: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Mon, 12 Aug 2019 23:51:43: #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 23:51:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:51:44: 20000000 INFO @ Mon, 12 Aug 2019 23:51:47: 23000000 INFO @ Mon, 12 Aug 2019 23:51:53: 21000000 INFO @ Mon, 12 Aug 2019 23:51:55: 24000000 INFO @ Mon, 12 Aug 2019 23:51:59: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:51:59: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:51:59: #1 total tags in treatment: 24561000 INFO @ Mon, 12 Aug 2019 23:51:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:51:59: #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 23:52:00: #1 tags after filtering in treatment: 24561000 INFO @ Mon, 12 Aug 2019 23:52:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:52:00: #1 finished! INFO @ Mon, 12 Aug 2019 23:52:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:52:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:52:02: 22000000 INFO @ Mon, 12 Aug 2019 23:52:02: #2 number of paired peaks: 311 WARNING @ Mon, 12 Aug 2019 23:52:02: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Mon, 12 Aug 2019 23:52:02: start model_add_line... INFO @ Mon, 12 Aug 2019 23:52:02: start X-correlation... INFO @ Mon, 12 Aug 2019 23:52:02: end of X-cor INFO @ Mon, 12 Aug 2019 23:52:02: #2 finished! INFO @ Mon, 12 Aug 2019 23:52:02: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 23:52:02: #2 alternative fragment length(s) may be 3,47 bps INFO @ Mon, 12 Aug 2019 23:52:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.20_model.r WARNING @ Mon, 12 Aug 2019 23:52:02: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:52:02: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Mon, 12 Aug 2019 23:52:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:52:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:52:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:52:11: 23000000 INFO @ Mon, 12 Aug 2019 23:52:19: 24000000 INFO @ Mon, 12 Aug 2019 23:52:24: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:52:24: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:52:24: #1 total tags in treatment: 24561000 INFO @ Mon, 12 Aug 2019 23:52:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:52:24: #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 23:52:25: #1 tags after filtering in treatment: 24561000 INFO @ Mon, 12 Aug 2019 23:52:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:52:25: #1 finished! INFO @ Mon, 12 Aug 2019 23:52:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:52:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:52:27: #2 number of paired peaks: 311 WARNING @ Mon, 12 Aug 2019 23:52:27: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Mon, 12 Aug 2019 23:52:27: start model_add_line... INFO @ Mon, 12 Aug 2019 23:52:27: start X-correlation... INFO @ Mon, 12 Aug 2019 23:52:27: end of X-cor INFO @ Mon, 12 Aug 2019 23:52:27: #2 finished! INFO @ Mon, 12 Aug 2019 23:52:27: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 23:52:27: #2 alternative fragment length(s) may be 3,47 bps INFO @ Mon, 12 Aug 2019 23:52:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.05_model.r WARNING @ Mon, 12 Aug 2019 23:52:27: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:52:27: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Mon, 12 Aug 2019 23:52:27: #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 23:52:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:52:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:52:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:53:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:53:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:53:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:53:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.10_summits.bed INFO @ Mon, 12 Aug 2019 23:53:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2122 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:53:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:53:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:53:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:53:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.20_summits.bed INFO @ Mon, 12 Aug 2019 23:53:31: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1185 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:53:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:53:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:53:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011041/SRX5011041.05_summits.bed INFO @ Mon, 12 Aug 2019 23:53:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3665 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。