Job ID = 1300742 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,041,555 reads read : 28,041,555 reads written : 28,041,555 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: 00:06:53 28041555 reads; of these: 28041555 (100.00%) were unpaired; of these: 9953927 (35.50%) aligned 0 times 13570850 (48.40%) aligned exactly 1 time 4516778 (16.11%) aligned >1 times 64.50% overall alignment rate Time searching: 00:06:53 Overall time: 00:06:53 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 8 files... [bam_rmdupse_core] 8760117 / 18087628 = 0.4843 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 19:40:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.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 19:40:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:40:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:40:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.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 19:40:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:40:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:40:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.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 19:40:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:40:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:40:17: 1000000 INFO @ Mon, 03 Jun 2019 19:40:18: 1000000 INFO @ Mon, 03 Jun 2019 19:40:18: 1000000 INFO @ Mon, 03 Jun 2019 19:40:25: 2000000 INFO @ Mon, 03 Jun 2019 19:40:26: 2000000 INFO @ Mon, 03 Jun 2019 19:40:26: 2000000 INFO @ Mon, 03 Jun 2019 19:40:32: 3000000 INFO @ Mon, 03 Jun 2019 19:40:34: 3000000 INFO @ Mon, 03 Jun 2019 19:40:34: 3000000 INFO @ Mon, 03 Jun 2019 19:40:39: 4000000 INFO @ Mon, 03 Jun 2019 19:40:42: 4000000 INFO @ Mon, 03 Jun 2019 19:40:42: 4000000 INFO @ Mon, 03 Jun 2019 19:40:47: 5000000 INFO @ Mon, 03 Jun 2019 19:40:49: 5000000 INFO @ Mon, 03 Jun 2019 19:40:50: 5000000 INFO @ Mon, 03 Jun 2019 19:40:55: 6000000 INFO @ Mon, 03 Jun 2019 19:40:58: 6000000 INFO @ Mon, 03 Jun 2019 19:40:58: 6000000 INFO @ Mon, 03 Jun 2019 19:41:02: 7000000 INFO @ Mon, 03 Jun 2019 19:41:05: 7000000 INFO @ Mon, 03 Jun 2019 19:41:06: 7000000 INFO @ Mon, 03 Jun 2019 19:41:10: 8000000 INFO @ Mon, 03 Jun 2019 19:41:13: 8000000 INFO @ Mon, 03 Jun 2019 19:41:14: 8000000 INFO @ Mon, 03 Jun 2019 19:41:17: 9000000 INFO @ Mon, 03 Jun 2019 19:41:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:41:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:41:19: #1 total tags in treatment: 9327511 INFO @ Mon, 03 Jun 2019 19:41:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:41:19: #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 19:41:19: #1 tags after filtering in treatment: 9327511 INFO @ Mon, 03 Jun 2019 19:41:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:41:19: #1 finished! INFO @ Mon, 03 Jun 2019 19:41:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:41:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:41:21: #2 number of paired peaks: 4159 INFO @ Mon, 03 Jun 2019 19:41:21: start model_add_line... INFO @ Mon, 03 Jun 2019 19:41:21: start X-correlation... INFO @ Mon, 03 Jun 2019 19:41:21: end of X-cor INFO @ Mon, 03 Jun 2019 19:41:21: #2 finished! INFO @ Mon, 03 Jun 2019 19:41:21: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 19:41:21: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 03 Jun 2019 19:41:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.10_model.r INFO @ Mon, 03 Jun 2019 19:41:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:41:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:41:21: 9000000 INFO @ Mon, 03 Jun 2019 19:41:21: 9000000 INFO @ Mon, 03 Jun 2019 19:41:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:41:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:41:24: #1 total tags in treatment: 9327511 INFO @ Mon, 03 Jun 2019 19:41:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:41:24: #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 19:41:24: #1 tags after filtering in treatment: 9327511 INFO @ Mon, 03 Jun 2019 19:41:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:41:24: #1 finished! INFO @ Mon, 03 Jun 2019 19:41:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:41:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:41:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:41:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:41:24: #1 total tags in treatment: 9327511 INFO @ Mon, 03 Jun 2019 19:41:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:41:24: #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 19:41:24: #1 tags after filtering in treatment: 9327511 INFO @ Mon, 03 Jun 2019 19:41:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:41:24: #1 finished! INFO @ Mon, 03 Jun 2019 19:41:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:41:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:41:25: #2 number of paired peaks: 4159 INFO @ Mon, 03 Jun 2019 19:41:25: start model_add_line... INFO @ Mon, 03 Jun 2019 19:41:25: start X-correlation... INFO @ Mon, 03 Jun 2019 19:41:25: end of X-cor INFO @ Mon, 03 Jun 2019 19:41:25: #2 finished! INFO @ Mon, 03 Jun 2019 19:41:25: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 19:41:25: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 03 Jun 2019 19:41:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.20_model.r INFO @ Mon, 03 Jun 2019 19:41:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:41:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:41:25: #2 number of paired peaks: 4159 INFO @ Mon, 03 Jun 2019 19:41:25: start model_add_line... INFO @ Mon, 03 Jun 2019 19:41:26: start X-correlation... INFO @ Mon, 03 Jun 2019 19:41:26: end of X-cor INFO @ Mon, 03 Jun 2019 19:41:26: #2 finished! INFO @ Mon, 03 Jun 2019 19:41:26: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 19:41:26: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 03 Jun 2019 19:41:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.05_model.r INFO @ Mon, 03 Jun 2019 19:41:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:41:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:41:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:41:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:41:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:42:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:42:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:42:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.10_summits.bed INFO @ Mon, 03 Jun 2019 19:42:08: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7001 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:42:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:42:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:42:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.20_summits.bed INFO @ Mon, 03 Jun 2019 19:42:12: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5642 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:42:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:42:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:42:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823792/SRX4823792.05_summits.bed INFO @ Mon, 03 Jun 2019 19:42:14: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8214 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。