Job ID = 1295123 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,250,410 reads read : 18,250,410 reads written : 18,250,410 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: 00:05:47 18250410 reads; of these: 18250410 (100.00%) were unpaired; of these: 1076370 (5.90%) aligned 0 times 12870113 (70.52%) aligned exactly 1 time 4303927 (23.58%) aligned >1 times 94.10% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 3746863 / 17174040 = 0.2182 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 12:21:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.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 12:21:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:21:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:21:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.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 12:21:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:21:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:21:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.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 12:21:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:21:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:21:17: 1000000 INFO @ Mon, 03 Jun 2019 12:21:19: 1000000 INFO @ Mon, 03 Jun 2019 12:21:19: 1000000 INFO @ Mon, 03 Jun 2019 12:21:26: 2000000 INFO @ Mon, 03 Jun 2019 12:21:28: 2000000 INFO @ Mon, 03 Jun 2019 12:21:28: 2000000 INFO @ Mon, 03 Jun 2019 12:21:36: 3000000 INFO @ Mon, 03 Jun 2019 12:21:37: 3000000 INFO @ Mon, 03 Jun 2019 12:21:39: 3000000 INFO @ Mon, 03 Jun 2019 12:21:46: 4000000 INFO @ Mon, 03 Jun 2019 12:21:47: 4000000 INFO @ Mon, 03 Jun 2019 12:21:49: 4000000 INFO @ Mon, 03 Jun 2019 12:21:56: 5000000 INFO @ Mon, 03 Jun 2019 12:21:57: 5000000 INFO @ Mon, 03 Jun 2019 12:22:00: 5000000 INFO @ Mon, 03 Jun 2019 12:22:07: 6000000 INFO @ Mon, 03 Jun 2019 12:22:07: 6000000 INFO @ Mon, 03 Jun 2019 12:22:10: 6000000 INFO @ Mon, 03 Jun 2019 12:22:17: 7000000 INFO @ Mon, 03 Jun 2019 12:22:17: 7000000 INFO @ Mon, 03 Jun 2019 12:22:21: 7000000 INFO @ Mon, 03 Jun 2019 12:22:28: 8000000 INFO @ Mon, 03 Jun 2019 12:22:28: 8000000 INFO @ Mon, 03 Jun 2019 12:22:31: 8000000 INFO @ Mon, 03 Jun 2019 12:22:38: 9000000 INFO @ Mon, 03 Jun 2019 12:22:38: 9000000 INFO @ Mon, 03 Jun 2019 12:22:42: 9000000 INFO @ Mon, 03 Jun 2019 12:22:48: 10000000 INFO @ Mon, 03 Jun 2019 12:22:48: 10000000 INFO @ Mon, 03 Jun 2019 12:22:52: 10000000 INFO @ Mon, 03 Jun 2019 12:22:58: 11000000 INFO @ Mon, 03 Jun 2019 12:22:58: 11000000 INFO @ Mon, 03 Jun 2019 12:23:02: 11000000 INFO @ Mon, 03 Jun 2019 12:23:08: 12000000 INFO @ Mon, 03 Jun 2019 12:23:08: 12000000 INFO @ Mon, 03 Jun 2019 12:23:13: 12000000 INFO @ Mon, 03 Jun 2019 12:23:17: 13000000 INFO @ Mon, 03 Jun 2019 12:23:18: 13000000 INFO @ Mon, 03 Jun 2019 12:23:22: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 12:23:22: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 12:23:22: #1 total tags in treatment: 13427177 INFO @ Mon, 03 Jun 2019 12:23:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:23:22: #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 12:23:22: #1 tags after filtering in treatment: 13427177 INFO @ Mon, 03 Jun 2019 12:23:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:23:22: #1 finished! INFO @ Mon, 03 Jun 2019 12:23:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:23:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:23:23: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 12:23:23: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 12:23:23: #1 total tags in treatment: 13427177 INFO @ Mon, 03 Jun 2019 12:23:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:23:23: #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 12:23:23: 13000000 INFO @ Mon, 03 Jun 2019 12:23:23: #1 tags after filtering in treatment: 13427177 INFO @ Mon, 03 Jun 2019 12:23:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:23:23: #1 finished! INFO @ Mon, 03 Jun 2019 12:23:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:23:24: #2 number of paired peaks: 7497 INFO @ Mon, 03 Jun 2019 12:23:24: start model_add_line... INFO @ Mon, 03 Jun 2019 12:23:24: start X-correlation... INFO @ Mon, 03 Jun 2019 12:23:25: end of X-cor INFO @ Mon, 03 Jun 2019 12:23:25: #2 finished! INFO @ Mon, 03 Jun 2019 12:23:25: #2 predicted fragment length is 187 bps INFO @ Mon, 03 Jun 2019 12:23:25: #2 alternative fragment length(s) may be 187 bps INFO @ Mon, 03 Jun 2019 12:23:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.05_model.r INFO @ Mon, 03 Jun 2019 12:23:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:23:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:23:25: #2 number of paired peaks: 7497 INFO @ Mon, 03 Jun 2019 12:23:25: start model_add_line... INFO @ Mon, 03 Jun 2019 12:23:26: start X-correlation... INFO @ Mon, 03 Jun 2019 12:23:26: end of X-cor INFO @ Mon, 03 Jun 2019 12:23:26: #2 finished! INFO @ Mon, 03 Jun 2019 12:23:26: #2 predicted fragment length is 187 bps INFO @ Mon, 03 Jun 2019 12:23:26: #2 alternative fragment length(s) may be 187 bps INFO @ Mon, 03 Jun 2019 12:23:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.20_model.r INFO @ Mon, 03 Jun 2019 12:23:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:23:27: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 12:23:27: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 12:23:27: #1 total tags in treatment: 13427177 INFO @ Mon, 03 Jun 2019 12:23:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:23:27: #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 12:23:28: #1 tags after filtering in treatment: 13427177 INFO @ Mon, 03 Jun 2019 12:23:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:23:28: #1 finished! INFO @ Mon, 03 Jun 2019 12:23:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:23:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:23:30: #2 number of paired peaks: 7497 INFO @ Mon, 03 Jun 2019 12:23:30: start model_add_line... INFO @ Mon, 03 Jun 2019 12:23:30: start X-correlation... INFO @ Mon, 03 Jun 2019 12:23:30: end of X-cor INFO @ Mon, 03 Jun 2019 12:23:30: #2 finished! INFO @ Mon, 03 Jun 2019 12:23:30: #2 predicted fragment length is 187 bps INFO @ Mon, 03 Jun 2019 12:23:30: #2 alternative fragment length(s) may be 187 bps INFO @ Mon, 03 Jun 2019 12:23:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.10_model.r INFO @ Mon, 03 Jun 2019 12:23:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:23:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:24:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:24:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:24:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:24:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:24:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:24:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.05_summits.bed INFO @ Mon, 03 Jun 2019 12:24:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:24:36: Done! INFO @ Mon, 03 Jun 2019 12:24:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:24:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.20_summits.bed INFO @ Mon, 03 Jun 2019 12:24:37: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (14051 records, 4 fields): 21 millis pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (6741 records, 4 fields): 13 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:24:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:24:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:24:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX326966/SRX326966.10_summits.bed INFO @ Mon, 03 Jun 2019 12:24:41: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (10951 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。