Job ID = 1301158 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,982,023 reads read : 26,982,023 reads written : 26,982,023 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: 00:08:39 26982023 reads; of these: 26982023 (100.00%) were unpaired; of these: 4676525 (17.33%) aligned 0 times 14879292 (55.15%) aligned exactly 1 time 7426206 (27.52%) aligned >1 times 82.67% overall alignment rate Time searching: 00:08:39 Overall time: 00:08:39 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] 9075249 / 22305498 = 0.4069 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 20:02:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.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 20:02:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:02:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:02:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.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 20:02:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:02:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:02:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.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 20:02:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:02:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:02:58: 1000000 INFO @ Mon, 03 Jun 2019 20:02:58: 1000000 INFO @ Mon, 03 Jun 2019 20:03:00: 1000000 INFO @ Mon, 03 Jun 2019 20:03:05: 2000000 INFO @ Mon, 03 Jun 2019 20:03:06: 2000000 INFO @ Mon, 03 Jun 2019 20:03:10: 2000000 INFO @ Mon, 03 Jun 2019 20:03:13: 3000000 INFO @ Mon, 03 Jun 2019 20:03:13: 3000000 INFO @ Mon, 03 Jun 2019 20:03:19: 3000000 INFO @ Mon, 03 Jun 2019 20:03:20: 4000000 INFO @ Mon, 03 Jun 2019 20:03:20: 4000000 INFO @ Mon, 03 Jun 2019 20:03:27: 5000000 INFO @ Mon, 03 Jun 2019 20:03:27: 5000000 INFO @ Mon, 03 Jun 2019 20:03:28: 4000000 INFO @ Mon, 03 Jun 2019 20:03:34: 6000000 INFO @ Mon, 03 Jun 2019 20:03:35: 6000000 INFO @ Mon, 03 Jun 2019 20:03:37: 5000000 INFO @ Mon, 03 Jun 2019 20:03:41: 7000000 INFO @ Mon, 03 Jun 2019 20:03:42: 7000000 INFO @ Mon, 03 Jun 2019 20:03:46: 6000000 INFO @ Mon, 03 Jun 2019 20:03:49: 8000000 INFO @ Mon, 03 Jun 2019 20:03:49: 8000000 INFO @ Mon, 03 Jun 2019 20:03:55: 7000000 INFO @ Mon, 03 Jun 2019 20:03:56: 9000000 INFO @ Mon, 03 Jun 2019 20:03:56: 9000000 INFO @ Mon, 03 Jun 2019 20:04:03: 10000000 INFO @ Mon, 03 Jun 2019 20:04:03: 10000000 INFO @ Mon, 03 Jun 2019 20:04:04: 8000000 INFO @ Mon, 03 Jun 2019 20:04:10: 11000000 INFO @ Mon, 03 Jun 2019 20:04:10: 11000000 INFO @ Mon, 03 Jun 2019 20:04:13: 9000000 INFO @ Mon, 03 Jun 2019 20:04:17: 12000000 INFO @ Mon, 03 Jun 2019 20:04:17: 12000000 INFO @ Mon, 03 Jun 2019 20:04:22: 10000000 INFO @ Mon, 03 Jun 2019 20:04:24: 13000000 INFO @ Mon, 03 Jun 2019 20:04:24: 13000000 INFO @ Mon, 03 Jun 2019 20:04:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:04:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:04:25: #1 total tags in treatment: 13230249 INFO @ Mon, 03 Jun 2019 20:04:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:04:25: #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 20:04:26: #1 tags after filtering in treatment: 13230249 INFO @ Mon, 03 Jun 2019 20:04:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:04:26: #1 finished! INFO @ Mon, 03 Jun 2019 20:04:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:04:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:04:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:04:26: #1 total tags in treatment: 13230249 INFO @ Mon, 03 Jun 2019 20:04:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:04:26: #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 20:04:26: #1 tags after filtering in treatment: 13230249 INFO @ Mon, 03 Jun 2019 20:04:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:04:26: #1 finished! INFO @ Mon, 03 Jun 2019 20:04:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:04:27: #2 number of paired peaks: 1212 INFO @ Mon, 03 Jun 2019 20:04:27: start model_add_line... INFO @ Mon, 03 Jun 2019 20:04:27: start X-correlation... INFO @ Mon, 03 Jun 2019 20:04:27: end of X-cor INFO @ Mon, 03 Jun 2019 20:04:27: #2 finished! INFO @ Mon, 03 Jun 2019 20:04:27: #2 predicted fragment length is 108 bps INFO @ Mon, 03 Jun 2019 20:04:27: #2 alternative fragment length(s) may be 4,108 bps INFO @ Mon, 03 Jun 2019 20:04:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.05_model.r INFO @ Mon, 03 Jun 2019 20:04:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:04:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:04:28: #2 number of paired peaks: 1212 INFO @ Mon, 03 Jun 2019 20:04:28: start model_add_line... INFO @ Mon, 03 Jun 2019 20:04:28: start X-correlation... INFO @ Mon, 03 Jun 2019 20:04:28: end of X-cor INFO @ Mon, 03 Jun 2019 20:04:28: #2 finished! INFO @ Mon, 03 Jun 2019 20:04:28: #2 predicted fragment length is 108 bps INFO @ Mon, 03 Jun 2019 20:04:28: #2 alternative fragment length(s) may be 4,108 bps INFO @ Mon, 03 Jun 2019 20:04:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.20_model.r INFO @ Mon, 03 Jun 2019 20:04:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:04:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:04:31: 11000000 INFO @ Mon, 03 Jun 2019 20:04:40: 12000000 INFO @ Mon, 03 Jun 2019 20:04:48: 13000000 INFO @ Mon, 03 Jun 2019 20:04:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:04:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:04:50: #1 total tags in treatment: 13230249 INFO @ Mon, 03 Jun 2019 20:04:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:04:50: #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 20:04:51: #1 tags after filtering in treatment: 13230249 INFO @ Mon, 03 Jun 2019 20:04:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:04:51: #1 finished! INFO @ Mon, 03 Jun 2019 20:04:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:04:52: #2 number of paired peaks: 1212 INFO @ Mon, 03 Jun 2019 20:04:52: start model_add_line... INFO @ Mon, 03 Jun 2019 20:04:52: start X-correlation... INFO @ Mon, 03 Jun 2019 20:04:52: end of X-cor INFO @ Mon, 03 Jun 2019 20:04:52: #2 finished! INFO @ Mon, 03 Jun 2019 20:04:52: #2 predicted fragment length is 108 bps INFO @ Mon, 03 Jun 2019 20:04:52: #2 alternative fragment length(s) may be 4,108 bps INFO @ Mon, 03 Jun 2019 20:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.10_model.r INFO @ Mon, 03 Jun 2019 20:04:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:05:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:05:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:05:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:05:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:05:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.20_summits.bed INFO @ Mon, 03 Jun 2019 20:05:25: Done! INFO @ Mon, 03 Jun 2019 20:05:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:05:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.05_peaks.narrowPeak pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1314 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:05:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.05_summits.bed INFO @ Mon, 03 Jun 2019 20:05:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4852 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:05:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:05:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:05:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:05:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485202/SRX485202.10_summits.bed INFO @ Mon, 03 Jun 2019 20:05:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2736 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。