Job ID = 1294207 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,978,622 reads read : 34,978,622 reads written : 34,978,622 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: 00:24:20 34978622 reads; of these: 34978622 (100.00%) were unpaired; of these: 609985 (1.74%) aligned 0 times 9020884 (25.79%) aligned exactly 1 time 25347753 (72.47%) aligned >1 times 98.26% overall alignment rate Time searching: 00:24:20 Overall time: 00:24:20 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] 11804920 / 34368637 = 0.3435 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 06:04:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.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 06:04:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:04:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:04:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.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 06:04:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:04:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:04:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.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 06:04:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:04:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:05:04: 1000000 INFO @ Mon, 03 Jun 2019 06:05:05: 1000000 INFO @ Mon, 03 Jun 2019 06:05:05: 1000000 INFO @ Mon, 03 Jun 2019 06:05:12: 2000000 INFO @ Mon, 03 Jun 2019 06:05:13: 2000000 INFO @ Mon, 03 Jun 2019 06:05:13: 2000000 INFO @ Mon, 03 Jun 2019 06:05:19: 3000000 INFO @ Mon, 03 Jun 2019 06:05:20: 3000000 INFO @ Mon, 03 Jun 2019 06:05:21: 3000000 INFO @ Mon, 03 Jun 2019 06:05:26: 4000000 INFO @ Mon, 03 Jun 2019 06:05:28: 4000000 INFO @ Mon, 03 Jun 2019 06:05:29: 4000000 INFO @ Mon, 03 Jun 2019 06:05:34: 5000000 INFO @ Mon, 03 Jun 2019 06:05:36: 5000000 INFO @ Mon, 03 Jun 2019 06:05:37: 5000000 INFO @ Mon, 03 Jun 2019 06:05:41: 6000000 INFO @ Mon, 03 Jun 2019 06:05:43: 6000000 INFO @ Mon, 03 Jun 2019 06:05:45: 6000000 INFO @ Mon, 03 Jun 2019 06:05:49: 7000000 INFO @ Mon, 03 Jun 2019 06:05:50: 7000000 INFO @ Mon, 03 Jun 2019 06:05:53: 7000000 INFO @ Mon, 03 Jun 2019 06:05:56: 8000000 INFO @ Mon, 03 Jun 2019 06:05:59: 8000000 INFO @ Mon, 03 Jun 2019 06:06:01: 8000000 INFO @ Mon, 03 Jun 2019 06:06:04: 9000000 INFO @ Mon, 03 Jun 2019 06:06:07: 9000000 INFO @ Mon, 03 Jun 2019 06:06:10: 9000000 INFO @ Mon, 03 Jun 2019 06:06:11: 10000000 INFO @ Mon, 03 Jun 2019 06:06:15: 10000000 INFO @ Mon, 03 Jun 2019 06:06:17: 10000000 INFO @ Mon, 03 Jun 2019 06:06:19: 11000000 INFO @ Mon, 03 Jun 2019 06:06:22: 11000000 INFO @ Mon, 03 Jun 2019 06:06:25: 11000000 INFO @ Mon, 03 Jun 2019 06:06:26: 12000000 INFO @ Mon, 03 Jun 2019 06:06:30: 12000000 INFO @ Mon, 03 Jun 2019 06:06:33: 12000000 INFO @ Mon, 03 Jun 2019 06:06:34: 13000000 INFO @ Mon, 03 Jun 2019 06:06:38: 13000000 INFO @ Mon, 03 Jun 2019 06:06:41: 14000000 INFO @ Mon, 03 Jun 2019 06:06:41: 13000000 INFO @ Mon, 03 Jun 2019 06:06:45: 14000000 INFO @ Mon, 03 Jun 2019 06:06:48: 15000000 INFO @ Mon, 03 Jun 2019 06:06:50: 14000000 INFO @ Mon, 03 Jun 2019 06:06:53: 15000000 INFO @ Mon, 03 Jun 2019 06:06:56: 16000000 INFO @ Mon, 03 Jun 2019 06:06:57: 15000000 INFO @ Mon, 03 Jun 2019 06:07:00: 16000000 INFO @ Mon, 03 Jun 2019 06:07:03: 17000000 INFO @ Mon, 03 Jun 2019 06:07:05: 16000000 INFO @ Mon, 03 Jun 2019 06:07:08: 17000000 INFO @ Mon, 03 Jun 2019 06:07:11: 18000000 INFO @ Mon, 03 Jun 2019 06:07:14: 17000000 INFO @ Mon, 03 Jun 2019 06:07:17: 18000000 INFO @ Mon, 03 Jun 2019 06:07:18: 19000000 INFO @ Mon, 03 Jun 2019 06:07:22: 18000000 INFO @ Mon, 03 Jun 2019 06:07:25: 19000000 INFO @ Mon, 03 Jun 2019 06:07:26: 20000000 INFO @ Mon, 03 Jun 2019 06:07:30: 19000000 INFO @ Mon, 03 Jun 2019 06:07:33: 20000000 INFO @ Mon, 03 Jun 2019 06:07:33: 21000000 INFO @ Mon, 03 Jun 2019 06:07:38: 20000000 INFO @ Mon, 03 Jun 2019 06:07:40: 22000000 INFO @ Mon, 03 Jun 2019 06:07:40: 21000000 INFO @ Mon, 03 Jun 2019 06:07:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 06:07:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 06:07:45: #1 total tags in treatment: 22563717 INFO @ Mon, 03 Jun 2019 06:07:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:07:45: #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 06:07:45: #1 tags after filtering in treatment: 22563717 INFO @ Mon, 03 Jun 2019 06:07:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:07:45: #1 finished! INFO @ Mon, 03 Jun 2019 06:07:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:07:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:07:46: 21000000 INFO @ Mon, 03 Jun 2019 06:07:47: #2 number of paired peaks: 1735 INFO @ Mon, 03 Jun 2019 06:07:47: start model_add_line... INFO @ Mon, 03 Jun 2019 06:07:48: start X-correlation... INFO @ Mon, 03 Jun 2019 06:07:48: end of X-cor INFO @ Mon, 03 Jun 2019 06:07:48: #2 finished! INFO @ Mon, 03 Jun 2019 06:07:48: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 06:07:48: #2 alternative fragment length(s) may be 3,53 bps INFO @ Mon, 03 Jun 2019 06:07:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.05_model.r WARNING @ Mon, 03 Jun 2019 06:07:48: #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, 03 Jun 2019 06:07:48: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Mon, 03 Jun 2019 06:07:48: #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 06:07:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:07:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:07:49: 22000000 INFO @ Mon, 03 Jun 2019 06:07:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 06:07:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 06:07:53: #1 total tags in treatment: 22563717 INFO @ Mon, 03 Jun 2019 06:07:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:07:53: #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 06:07:54: #1 tags after filtering in treatment: 22563717 INFO @ Mon, 03 Jun 2019 06:07:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:07:54: #1 finished! INFO @ Mon, 03 Jun 2019 06:07:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:07:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:07:55: 22000000 INFO @ Mon, 03 Jun 2019 06:07:56: #2 number of paired peaks: 1735 INFO @ Mon, 03 Jun 2019 06:07:56: start model_add_line... INFO @ Mon, 03 Jun 2019 06:07:56: start X-correlation... INFO @ Mon, 03 Jun 2019 06:07:56: end of X-cor INFO @ Mon, 03 Jun 2019 06:07:56: #2 finished! INFO @ Mon, 03 Jun 2019 06:07:56: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 06:07:56: #2 alternative fragment length(s) may be 3,53 bps INFO @ Mon, 03 Jun 2019 06:07:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.10_model.r WARNING @ Mon, 03 Jun 2019 06:07:56: #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, 03 Jun 2019 06:07:56: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Mon, 03 Jun 2019 06:07:56: #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 06:07:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:07:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:08:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 06:08:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 06:08:00: #1 total tags in treatment: 22563717 INFO @ Mon, 03 Jun 2019 06:08:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:08:00: #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 06:08:00: #1 tags after filtering in treatment: 22563717 INFO @ Mon, 03 Jun 2019 06:08:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:08:00: #1 finished! INFO @ Mon, 03 Jun 2019 06:08:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:08:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:08:03: #2 number of paired peaks: 1735 INFO @ Mon, 03 Jun 2019 06:08:03: start model_add_line... INFO @ Mon, 03 Jun 2019 06:08:03: start X-correlation... INFO @ Mon, 03 Jun 2019 06:08:03: end of X-cor INFO @ Mon, 03 Jun 2019 06:08:03: #2 finished! INFO @ Mon, 03 Jun 2019 06:08:03: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 06:08:03: #2 alternative fragment length(s) may be 3,53 bps INFO @ Mon, 03 Jun 2019 06:08:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.20_model.r WARNING @ Mon, 03 Jun 2019 06:08:03: #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, 03 Jun 2019 06:08:03: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Mon, 03 Jun 2019 06:08:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:08:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:08:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:08:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:08:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:08:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:09:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:09:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:09:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.05_summits.bed INFO @ Mon, 03 Jun 2019 06:09:09: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (20165 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:09:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:09:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:09:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.10_summits.bed INFO @ Mon, 03 Jun 2019 06:09:18: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8786 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:09:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:09:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:09:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201885/SRX201885.20_summits.bed INFO @ Mon, 03 Jun 2019 06:09:24: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2355 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。