Job ID = 1294144 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 41,858,082 reads read : 41,858,082 reads written : 41,858,082 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:27 41858082 reads; of these: 41858082 (100.00%) were unpaired; of these: 1433170 (3.42%) aligned 0 times 33906453 (81.00%) aligned exactly 1 time 6518459 (15.57%) aligned >1 times 96.58% overall alignment rate Time searching: 00:12:27 Overall time: 00:12:27 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 20 files... [bam_rmdupse_core] 11007822 / 40424912 = 0.2723 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, 03 Jun 2019 05:29:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.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, 03 Jun 2019 05:29:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:29:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:29:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.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, 03 Jun 2019 05:29:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:29:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:29:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.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, 03 Jun 2019 05:29:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:29:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:29:13: 1000000 INFO @ Mon, 03 Jun 2019 05:29:14: 1000000 INFO @ Mon, 03 Jun 2019 05:29:16: 1000000 INFO @ Mon, 03 Jun 2019 05:29:21: 2000000 INFO @ Mon, 03 Jun 2019 05:29:24: 2000000 INFO @ Mon, 03 Jun 2019 05:29:27: 2000000 INFO @ Mon, 03 Jun 2019 05:29:29: 3000000 INFO @ Mon, 03 Jun 2019 05:29:33: 3000000 INFO @ Mon, 03 Jun 2019 05:29:37: 4000000 INFO @ Mon, 03 Jun 2019 05:29:38: 3000000 INFO @ Mon, 03 Jun 2019 05:29:42: 4000000 INFO @ Mon, 03 Jun 2019 05:29:45: 5000000 INFO @ Mon, 03 Jun 2019 05:29:49: 4000000 INFO @ Mon, 03 Jun 2019 05:29:52: 5000000 INFO @ Mon, 03 Jun 2019 05:29:53: 6000000 INFO @ Mon, 03 Jun 2019 05:30:00: 5000000 INFO @ Mon, 03 Jun 2019 05:30:01: 7000000 INFO @ Mon, 03 Jun 2019 05:30:01: 6000000 INFO @ Mon, 03 Jun 2019 05:30:09: 8000000 INFO @ Mon, 03 Jun 2019 05:30:10: 7000000 INFO @ Mon, 03 Jun 2019 05:30:12: 6000000 INFO @ Mon, 03 Jun 2019 05:30:17: 9000000 INFO @ Mon, 03 Jun 2019 05:30:19: 8000000 INFO @ Mon, 03 Jun 2019 05:30:24: 7000000 INFO @ Mon, 03 Jun 2019 05:30:25: 10000000 INFO @ Mon, 03 Jun 2019 05:30:29: 9000000 INFO @ Mon, 03 Jun 2019 05:30:32: 11000000 INFO @ Mon, 03 Jun 2019 05:30:35: 8000000 INFO @ Mon, 03 Jun 2019 05:30:38: 10000000 INFO @ Mon, 03 Jun 2019 05:30:40: 12000000 INFO @ Mon, 03 Jun 2019 05:30:47: 9000000 INFO @ Mon, 03 Jun 2019 05:30:47: 11000000 INFO @ Mon, 03 Jun 2019 05:30:48: 13000000 INFO @ Mon, 03 Jun 2019 05:30:56: 14000000 INFO @ Mon, 03 Jun 2019 05:30:57: 12000000 INFO @ Mon, 03 Jun 2019 05:30:58: 10000000 INFO @ Mon, 03 Jun 2019 05:31:04: 15000000 INFO @ Mon, 03 Jun 2019 05:31:06: 13000000 INFO @ Mon, 03 Jun 2019 05:31:10: 11000000 INFO @ Mon, 03 Jun 2019 05:31:12: 16000000 INFO @ Mon, 03 Jun 2019 05:31:15: 14000000 INFO @ Mon, 03 Jun 2019 05:31:20: 17000000 INFO @ Mon, 03 Jun 2019 05:31:22: 12000000 INFO @ Mon, 03 Jun 2019 05:31:25: 15000000 INFO @ Mon, 03 Jun 2019 05:31:28: 18000000 INFO @ Mon, 03 Jun 2019 05:31:34: 13000000 INFO @ Mon, 03 Jun 2019 05:31:34: 16000000 INFO @ Mon, 03 Jun 2019 05:31:36: 19000000 INFO @ Mon, 03 Jun 2019 05:31:43: 17000000 INFO @ Mon, 03 Jun 2019 05:31:44: 20000000 INFO @ Mon, 03 Jun 2019 05:31:45: 14000000 INFO @ Mon, 03 Jun 2019 05:31:52: 21000000 INFO @ Mon, 03 Jun 2019 05:31:52: 18000000 INFO @ Mon, 03 Jun 2019 05:31:57: 15000000 INFO @ Mon, 03 Jun 2019 05:32:00: 22000000 INFO @ Mon, 03 Jun 2019 05:32:02: 19000000 INFO @ Mon, 03 Jun 2019 05:32:07: 16000000 INFO @ Mon, 03 Jun 2019 05:32:08: 23000000 INFO @ Mon, 03 Jun 2019 05:32:11: 20000000 INFO @ Mon, 03 Jun 2019 05:32:16: 24000000 INFO @ Mon, 03 Jun 2019 05:32:18: 17000000 INFO @ Mon, 03 Jun 2019 05:32:20: 21000000 INFO @ Mon, 03 Jun 2019 05:32:24: 25000000 INFO @ Mon, 03 Jun 2019 05:32:29: 18000000 INFO @ Mon, 03 Jun 2019 05:32:30: 22000000 INFO @ Mon, 03 Jun 2019 05:32:32: 26000000 INFO @ Mon, 03 Jun 2019 05:32:39: 23000000 INFO @ Mon, 03 Jun 2019 05:32:40: 19000000 INFO @ Mon, 03 Jun 2019 05:32:40: 27000000 INFO @ Mon, 03 Jun 2019 05:32:48: 24000000 INFO @ Mon, 03 Jun 2019 05:32:48: 28000000 INFO @ Mon, 03 Jun 2019 05:32:51: 20000000 INFO @ Mon, 03 Jun 2019 05:32:56: 29000000 INFO @ Mon, 03 Jun 2019 05:32:57: 25000000 INFO @ Mon, 03 Jun 2019 05:33:00: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:33:00: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:33:00: #1 total tags in treatment: 29417090 INFO @ Mon, 03 Jun 2019 05:33:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:33:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:33:00: #1 tags after filtering in treatment: 29417090 INFO @ Mon, 03 Jun 2019 05:33:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:33:00: #1 finished! INFO @ Mon, 03 Jun 2019 05:33:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:33:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:33:01: 21000000 INFO @ Mon, 03 Jun 2019 05:33:03: #2 number of paired peaks: 2009 INFO @ Mon, 03 Jun 2019 05:33:03: start model_add_line... INFO @ Mon, 03 Jun 2019 05:33:03: start X-correlation... INFO @ Mon, 03 Jun 2019 05:33:04: end of X-cor INFO @ Mon, 03 Jun 2019 05:33:04: #2 finished! INFO @ Mon, 03 Jun 2019 05:33:04: #2 predicted fragment length is 102 bps INFO @ Mon, 03 Jun 2019 05:33:04: #2 alternative fragment length(s) may be 3,102 bps INFO @ Mon, 03 Jun 2019 05:33:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.10_model.r WARNING @ Mon, 03 Jun 2019 05:33:04: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:33:04: #2 You may need to consider one of the other alternative d(s): 3,102 WARNING @ Mon, 03 Jun 2019 05:33:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:33:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:33:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:33:07: 26000000 INFO @ Mon, 03 Jun 2019 05:33:12: 22000000 INFO @ Mon, 03 Jun 2019 05:33:16: 27000000 INFO @ Mon, 03 Jun 2019 05:33:23: 23000000 INFO @ Mon, 03 Jun 2019 05:33:25: 28000000 INFO @ Mon, 03 Jun 2019 05:33:34: 24000000 INFO @ Mon, 03 Jun 2019 05:33:35: 29000000 INFO @ Mon, 03 Jun 2019 05:33:39: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:33:39: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:33:39: #1 total tags in treatment: 29417090 INFO @ Mon, 03 Jun 2019 05:33:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:33:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:33:39: #1 tags after filtering in treatment: 29417090 INFO @ Mon, 03 Jun 2019 05:33:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:33:39: #1 finished! INFO @ Mon, 03 Jun 2019 05:33:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:33:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:33:42: #2 number of paired peaks: 2009 INFO @ Mon, 03 Jun 2019 05:33:42: start model_add_line... INFO @ Mon, 03 Jun 2019 05:33:42: start X-correlation... INFO @ Mon, 03 Jun 2019 05:33:42: end of X-cor INFO @ Mon, 03 Jun 2019 05:33:42: #2 finished! INFO @ Mon, 03 Jun 2019 05:33:42: #2 predicted fragment length is 102 bps INFO @ Mon, 03 Jun 2019 05:33:42: #2 alternative fragment length(s) may be 3,102 bps INFO @ Mon, 03 Jun 2019 05:33:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.05_model.r WARNING @ Mon, 03 Jun 2019 05:33:42: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:33:42: #2 You may need to consider one of the other alternative d(s): 3,102 WARNING @ Mon, 03 Jun 2019 05:33:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:33:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:33:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:33:44: 25000000 INFO @ Mon, 03 Jun 2019 05:33:55: 26000000 INFO @ Mon, 03 Jun 2019 05:34:05: 27000000 INFO @ Mon, 03 Jun 2019 05:34:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:34:16: 28000000 INFO @ Mon, 03 Jun 2019 05:34:26: 29000000 INFO @ Mon, 03 Jun 2019 05:34:30: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:34:30: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:34:30: #1 total tags in treatment: 29417090 INFO @ Mon, 03 Jun 2019 05:34:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:34:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:34:31: #1 tags after filtering in treatment: 29417090 INFO @ Mon, 03 Jun 2019 05:34:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:34:31: #1 finished! INFO @ Mon, 03 Jun 2019 05:34:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:34:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:34:34: #2 number of paired peaks: 2009 INFO @ Mon, 03 Jun 2019 05:34:34: start model_add_line... INFO @ Mon, 03 Jun 2019 05:34:34: start X-correlation... INFO @ Mon, 03 Jun 2019 05:34:34: end of X-cor INFO @ Mon, 03 Jun 2019 05:34:34: #2 finished! INFO @ Mon, 03 Jun 2019 05:34:34: #2 predicted fragment length is 102 bps INFO @ Mon, 03 Jun 2019 05:34:34: #2 alternative fragment length(s) may be 3,102 bps INFO @ Mon, 03 Jun 2019 05:34:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.20_model.r WARNING @ Mon, 03 Jun 2019 05:34:34: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:34:34: #2 You may need to consider one of the other alternative d(s): 3,102 WARNING @ Mon, 03 Jun 2019 05:34:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:34:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:34:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:34:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:34:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:34:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.10_summits.bed INFO @ Mon, 03 Jun 2019 05:34:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10675 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:34:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:35:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:35:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:35:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.05_summits.bed INFO @ Mon, 03 Jun 2019 05:35:24: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (20247 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:35:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:36:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:36:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:36:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193322/SRX193322.20_summits.bed INFO @ Mon, 03 Jun 2019 05:36:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3389 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。