Job ID = 1294708 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,144,533 reads read : 24,144,533 reads written : 24,144,533 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: 00:06:19 24144533 reads; of these: 24144533 (100.00%) were unpaired; of these: 1128975 (4.68%) aligned 0 times 21245146 (87.99%) aligned exactly 1 time 1770412 (7.33%) aligned >1 times 95.32% overall alignment rate Time searching: 00:06:19 Overall time: 00:06:19 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] 10736493 / 23015558 = 0.4665 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 10:05:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.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 10:05:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:05:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:05:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.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 10:05:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:05:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:05:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.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 10:05:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:05:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:05:33: 1000000 INFO @ Mon, 03 Jun 2019 10:05:33: 1000000 INFO @ Mon, 03 Jun 2019 10:05:35: 1000000 INFO @ Mon, 03 Jun 2019 10:05:40: 2000000 INFO @ Mon, 03 Jun 2019 10:05:41: 2000000 INFO @ Mon, 03 Jun 2019 10:05:44: 2000000 INFO @ Mon, 03 Jun 2019 10:05:48: 3000000 INFO @ Mon, 03 Jun 2019 10:05:49: 3000000 INFO @ Mon, 03 Jun 2019 10:05:53: 3000000 INFO @ Mon, 03 Jun 2019 10:05:55: 4000000 INFO @ Mon, 03 Jun 2019 10:05:57: 4000000 INFO @ Mon, 03 Jun 2019 10:06:02: 4000000 INFO @ Mon, 03 Jun 2019 10:06:03: 5000000 INFO @ Mon, 03 Jun 2019 10:06:04: 5000000 INFO @ Mon, 03 Jun 2019 10:06:11: 6000000 INFO @ Mon, 03 Jun 2019 10:06:12: 6000000 INFO @ Mon, 03 Jun 2019 10:06:12: 5000000 INFO @ Mon, 03 Jun 2019 10:06:18: 7000000 INFO @ Mon, 03 Jun 2019 10:06:20: 7000000 INFO @ Mon, 03 Jun 2019 10:06:22: 6000000 INFO @ Mon, 03 Jun 2019 10:06:26: 8000000 INFO @ Mon, 03 Jun 2019 10:06:28: 8000000 INFO @ Mon, 03 Jun 2019 10:06:31: 7000000 INFO @ Mon, 03 Jun 2019 10:06:33: 9000000 INFO @ Mon, 03 Jun 2019 10:06:36: 9000000 INFO @ Mon, 03 Jun 2019 10:06:40: 8000000 INFO @ Mon, 03 Jun 2019 10:06:40: 10000000 INFO @ Mon, 03 Jun 2019 10:06:44: 10000000 INFO @ Mon, 03 Jun 2019 10:06:48: 11000000 INFO @ Mon, 03 Jun 2019 10:06:49: 9000000 INFO @ Mon, 03 Jun 2019 10:06:52: 11000000 INFO @ Mon, 03 Jun 2019 10:06:55: 12000000 INFO @ Mon, 03 Jun 2019 10:06:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:06:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:06:58: #1 total tags in treatment: 12279065 INFO @ Mon, 03 Jun 2019 10:06:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:06:58: #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 10:06:58: #1 tags after filtering in treatment: 12279065 INFO @ Mon, 03 Jun 2019 10:06:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:06:58: #1 finished! INFO @ Mon, 03 Jun 2019 10:06:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:06:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:06:58: 10000000 INFO @ Mon, 03 Jun 2019 10:06:59: 12000000 INFO @ Mon, 03 Jun 2019 10:07:00: #2 number of paired peaks: 10811 INFO @ Mon, 03 Jun 2019 10:07:00: start model_add_line... INFO @ Mon, 03 Jun 2019 10:07:00: start X-correlation... INFO @ Mon, 03 Jun 2019 10:07:00: end of X-cor INFO @ Mon, 03 Jun 2019 10:07:00: #2 finished! INFO @ Mon, 03 Jun 2019 10:07:00: #2 predicted fragment length is 207 bps INFO @ Mon, 03 Jun 2019 10:07:00: #2 alternative fragment length(s) may be 207 bps INFO @ Mon, 03 Jun 2019 10:07:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.20_model.r INFO @ Mon, 03 Jun 2019 10:07:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:07:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:07:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:07:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:07:01: #1 total tags in treatment: 12279065 INFO @ Mon, 03 Jun 2019 10:07:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:07:01: #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 10:07:02: #1 tags after filtering in treatment: 12279065 INFO @ Mon, 03 Jun 2019 10:07:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:07:02: #1 finished! INFO @ Mon, 03 Jun 2019 10:07:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:07:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:07:04: #2 number of paired peaks: 10811 INFO @ Mon, 03 Jun 2019 10:07:04: start model_add_line... INFO @ Mon, 03 Jun 2019 10:07:04: start X-correlation... INFO @ Mon, 03 Jun 2019 10:07:04: end of X-cor INFO @ Mon, 03 Jun 2019 10:07:04: #2 finished! INFO @ Mon, 03 Jun 2019 10:07:04: #2 predicted fragment length is 207 bps INFO @ Mon, 03 Jun 2019 10:07:04: #2 alternative fragment length(s) may be 207 bps INFO @ Mon, 03 Jun 2019 10:07:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.05_model.r INFO @ Mon, 03 Jun 2019 10:07:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:07:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:07:07: 11000000 INFO @ Mon, 03 Jun 2019 10:07:16: 12000000 INFO @ Mon, 03 Jun 2019 10:07:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:07:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:07:18: #1 total tags in treatment: 12279065 INFO @ Mon, 03 Jun 2019 10:07:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:07:18: #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 10:07:19: #1 tags after filtering in treatment: 12279065 INFO @ Mon, 03 Jun 2019 10:07:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:07:19: #1 finished! INFO @ Mon, 03 Jun 2019 10:07:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:07:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:07:21: #2 number of paired peaks: 10811 INFO @ Mon, 03 Jun 2019 10:07:21: start model_add_line... INFO @ Mon, 03 Jun 2019 10:07:21: start X-correlation... INFO @ Mon, 03 Jun 2019 10:07:21: end of X-cor INFO @ Mon, 03 Jun 2019 10:07:21: #2 finished! INFO @ Mon, 03 Jun 2019 10:07:21: #2 predicted fragment length is 207 bps INFO @ Mon, 03 Jun 2019 10:07:21: #2 alternative fragment length(s) may be 207 bps INFO @ Mon, 03 Jun 2019 10:07:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.10_model.r INFO @ Mon, 03 Jun 2019 10:07:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:07:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:07:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:07:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:08:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:08:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:08:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.20_summits.bed INFO @ Mon, 03 Jun 2019 10:08:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7351 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:08:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:08:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:08:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:08:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.05_summits.bed INFO @ Mon, 03 Jun 2019 10:08:08: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8821 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 10:08:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:08:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:08:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287836/SRX287836.10_summits.bed INFO @ Mon, 03 Jun 2019 10:08:25: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (8186 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。