Job ID = 1293294 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 37,937,752 reads read : 37,937,752 reads written : 37,937,752 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: 00:10:30 37937752 reads; of these: 37937752 (100.00%) were unpaired; of these: 2050513 (5.40%) aligned 0 times 27786642 (73.24%) aligned exactly 1 time 8100597 (21.35%) aligned >1 times 94.60% overall alignment rate Time searching: 00:10:30 Overall time: 00:10:30 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] 12100617 / 35887239 = 0.3372 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 @ Sun, 02 Jun 2019 23:22:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.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 @ Sun, 02 Jun 2019 23:22:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:22:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:22:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.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 @ Sun, 02 Jun 2019 23:22:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:22:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:22:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.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 @ Sun, 02 Jun 2019 23:22:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:22:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:22:58: 1000000 INFO @ Sun, 02 Jun 2019 23:22:59: 1000000 INFO @ Sun, 02 Jun 2019 23:22:59: 1000000 INFO @ Sun, 02 Jun 2019 23:23:08: 2000000 INFO @ Sun, 02 Jun 2019 23:23:10: 2000000 INFO @ Sun, 02 Jun 2019 23:23:10: 2000000 INFO @ Sun, 02 Jun 2019 23:23:17: 3000000 INFO @ Sun, 02 Jun 2019 23:23:21: 3000000 INFO @ Sun, 02 Jun 2019 23:23:21: 3000000 INFO @ Sun, 02 Jun 2019 23:23:26: 4000000 INFO @ Sun, 02 Jun 2019 23:23:31: 4000000 INFO @ Sun, 02 Jun 2019 23:23:31: 4000000 INFO @ Sun, 02 Jun 2019 23:23:35: 5000000 INFO @ Sun, 02 Jun 2019 23:23:42: 5000000 INFO @ Sun, 02 Jun 2019 23:23:42: 5000000 INFO @ Sun, 02 Jun 2019 23:23:45: 6000000 INFO @ Sun, 02 Jun 2019 23:23:52: 6000000 INFO @ Sun, 02 Jun 2019 23:23:52: 6000000 INFO @ Sun, 02 Jun 2019 23:23:54: 7000000 INFO @ Sun, 02 Jun 2019 23:24:03: 7000000 INFO @ Sun, 02 Jun 2019 23:24:03: 7000000 INFO @ Sun, 02 Jun 2019 23:24:03: 8000000 INFO @ Sun, 02 Jun 2019 23:24:12: 9000000 INFO @ Sun, 02 Jun 2019 23:24:13: 8000000 INFO @ Sun, 02 Jun 2019 23:24:14: 8000000 INFO @ Sun, 02 Jun 2019 23:24:22: 10000000 INFO @ Sun, 02 Jun 2019 23:24:24: 9000000 INFO @ Sun, 02 Jun 2019 23:24:25: 9000000 INFO @ Sun, 02 Jun 2019 23:24:32: 11000000 INFO @ Sun, 02 Jun 2019 23:24:35: 10000000 INFO @ Sun, 02 Jun 2019 23:24:35: 10000000 INFO @ Sun, 02 Jun 2019 23:24:41: 12000000 INFO @ Sun, 02 Jun 2019 23:24:45: 11000000 INFO @ Sun, 02 Jun 2019 23:24:45: 11000000 INFO @ Sun, 02 Jun 2019 23:24:50: 13000000 INFO @ Sun, 02 Jun 2019 23:24:55: 12000000 INFO @ Sun, 02 Jun 2019 23:24:55: 12000000 INFO @ Sun, 02 Jun 2019 23:24:59: 14000000 INFO @ Sun, 02 Jun 2019 23:25:04: 13000000 INFO @ Sun, 02 Jun 2019 23:25:05: 13000000 INFO @ Sun, 02 Jun 2019 23:25:08: 15000000 INFO @ Sun, 02 Jun 2019 23:25:14: 14000000 INFO @ Sun, 02 Jun 2019 23:25:15: 14000000 INFO @ Sun, 02 Jun 2019 23:25:17: 16000000 INFO @ Sun, 02 Jun 2019 23:25:24: 15000000 INFO @ Sun, 02 Jun 2019 23:25:25: 15000000 INFO @ Sun, 02 Jun 2019 23:25:26: 17000000 INFO @ Sun, 02 Jun 2019 23:25:34: 16000000 INFO @ Sun, 02 Jun 2019 23:25:35: 16000000 INFO @ Sun, 02 Jun 2019 23:25:35: 18000000 INFO @ Sun, 02 Jun 2019 23:25:44: 17000000 INFO @ Sun, 02 Jun 2019 23:25:45: 19000000 INFO @ Sun, 02 Jun 2019 23:25:45: 17000000 INFO @ Sun, 02 Jun 2019 23:25:54: 20000000 INFO @ Sun, 02 Jun 2019 23:25:54: 18000000 INFO @ Sun, 02 Jun 2019 23:25:55: 18000000 INFO @ Sun, 02 Jun 2019 23:26:03: 21000000 INFO @ Sun, 02 Jun 2019 23:26:05: 19000000 INFO @ Sun, 02 Jun 2019 23:26:05: 19000000 INFO @ Sun, 02 Jun 2019 23:26:14: 22000000 INFO @ Sun, 02 Jun 2019 23:26:16: 20000000 INFO @ Sun, 02 Jun 2019 23:26:16: 20000000 INFO @ Sun, 02 Jun 2019 23:26:24: 23000000 INFO @ Sun, 02 Jun 2019 23:26:27: 21000000 INFO @ Sun, 02 Jun 2019 23:26:27: 21000000 INFO @ Sun, 02 Jun 2019 23:26:31: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:26:31: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:26:31: #1 total tags in treatment: 23786622 INFO @ Sun, 02 Jun 2019 23:26:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:26:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:26:32: #1 tags after filtering in treatment: 23786622 INFO @ Sun, 02 Jun 2019 23:26:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:26:32: #1 finished! INFO @ Sun, 02 Jun 2019 23:26:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:26:34: #2 number of paired peaks: 2792 INFO @ Sun, 02 Jun 2019 23:26:34: start model_add_line... INFO @ Sun, 02 Jun 2019 23:26:35: start X-correlation... INFO @ Sun, 02 Jun 2019 23:26:35: end of X-cor INFO @ Sun, 02 Jun 2019 23:26:35: #2 finished! INFO @ Sun, 02 Jun 2019 23:26:35: #2 predicted fragment length is 148 bps INFO @ Sun, 02 Jun 2019 23:26:35: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 02 Jun 2019 23:26:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.20_model.r INFO @ Sun, 02 Jun 2019 23:26:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:26:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:26:37: 22000000 INFO @ Sun, 02 Jun 2019 23:26:37: 22000000 INFO @ Sun, 02 Jun 2019 23:26:47: 23000000 INFO @ Sun, 02 Jun 2019 23:26:47: 23000000 INFO @ Sun, 02 Jun 2019 23:26:55: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:26:55: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:26:55: #1 total tags in treatment: 23786622 INFO @ Sun, 02 Jun 2019 23:26:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:26:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:26:55: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:26:55: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:26:55: #1 total tags in treatment: 23786622 INFO @ Sun, 02 Jun 2019 23:26:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:26:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:26:55: #1 tags after filtering in treatment: 23786622 INFO @ Sun, 02 Jun 2019 23:26:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:26:55: #1 finished! INFO @ Sun, 02 Jun 2019 23:26:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:26:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:26:55: #1 tags after filtering in treatment: 23786622 INFO @ Sun, 02 Jun 2019 23:26:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:26:55: #1 finished! INFO @ Sun, 02 Jun 2019 23:26:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:26:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:26:58: #2 number of paired peaks: 2792 INFO @ Sun, 02 Jun 2019 23:26:58: start model_add_line... INFO @ Sun, 02 Jun 2019 23:26:58: #2 number of paired peaks: 2792 INFO @ Sun, 02 Jun 2019 23:26:58: start model_add_line... INFO @ Sun, 02 Jun 2019 23:26:58: start X-correlation... INFO @ Sun, 02 Jun 2019 23:26:58: end of X-cor INFO @ Sun, 02 Jun 2019 23:26:58: #2 finished! INFO @ Sun, 02 Jun 2019 23:26:58: #2 predicted fragment length is 148 bps INFO @ Sun, 02 Jun 2019 23:26:58: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 02 Jun 2019 23:26:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.10_model.r INFO @ Sun, 02 Jun 2019 23:26:58: start X-correlation... INFO @ Sun, 02 Jun 2019 23:26:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:26:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:26:58: end of X-cor INFO @ Sun, 02 Jun 2019 23:26:58: #2 finished! INFO @ Sun, 02 Jun 2019 23:26:58: #2 predicted fragment length is 148 bps INFO @ Sun, 02 Jun 2019 23:26:58: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 02 Jun 2019 23:26:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.05_model.r INFO @ Sun, 02 Jun 2019 23:26:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:26:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:27:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:28:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:28:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:28:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:28:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:28:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.20_summits.bed INFO @ Sun, 02 Jun 2019 23:28:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7981 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:28:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:28:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:28:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.10_summits.bed INFO @ Sun, 02 Jun 2019 23:28:35: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10560 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:28:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:28:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:28:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX088859/ERX088859.05_summits.bed INFO @ Sun, 02 Jun 2019 23:28:36: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (13012 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。