Job ID = 1294219 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 40,933,550 reads read : 40,933,550 reads written : 40,933,550 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: 00:19:43 40933550 reads; of these: 40933550 (100.00%) were unpaired; of these: 1181681 (2.89%) aligned 0 times 31762886 (77.60%) aligned exactly 1 time 7988983 (19.52%) aligned >1 times 97.11% overall alignment rate Time searching: 00:19:43 Overall time: 00:19:43 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 20 files... [bam_rmdupse_core] 31062274 / 39751869 = 0.7814 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 06:09:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.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 06:09:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:09:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:09:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.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 06:09:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:09:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:09:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.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 06:09:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:09:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:09:30: 1000000 INFO @ Mon, 03 Jun 2019 06:09:31: 1000000 INFO @ Mon, 03 Jun 2019 06:09:34: 1000000 INFO @ Mon, 03 Jun 2019 06:09:39: 2000000 INFO @ Mon, 03 Jun 2019 06:09:41: 2000000 INFO @ Mon, 03 Jun 2019 06:09:46: 2000000 INFO @ Mon, 03 Jun 2019 06:09:48: 3000000 INFO @ Mon, 03 Jun 2019 06:09:51: 3000000 INFO @ Mon, 03 Jun 2019 06:09:58: 4000000 INFO @ Mon, 03 Jun 2019 06:09:59: 3000000 INFO @ Mon, 03 Jun 2019 06:10:01: 4000000 INFO @ Mon, 03 Jun 2019 06:10:07: 5000000 INFO @ Mon, 03 Jun 2019 06:10:11: 5000000 INFO @ Mon, 03 Jun 2019 06:10:11: 4000000 INFO @ Mon, 03 Jun 2019 06:10:15: 6000000 INFO @ Mon, 03 Jun 2019 06:10:21: 6000000 INFO @ Mon, 03 Jun 2019 06:10:24: 5000000 INFO @ Mon, 03 Jun 2019 06:10:24: 7000000 INFO @ Mon, 03 Jun 2019 06:10:31: 7000000 INFO @ Mon, 03 Jun 2019 06:10:33: 8000000 INFO @ Mon, 03 Jun 2019 06:10:36: 6000000 INFO @ Mon, 03 Jun 2019 06:10:39: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 06:10:39: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 06:10:39: #1 total tags in treatment: 8689595 INFO @ Mon, 03 Jun 2019 06:10:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:10:39: #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 06:10:40: #1 tags after filtering in treatment: 8689595 INFO @ Mon, 03 Jun 2019 06:10:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:10:40: #1 finished! INFO @ Mon, 03 Jun 2019 06:10:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:10:41: 8000000 INFO @ Mon, 03 Jun 2019 06:10:41: #2 number of paired peaks: 7270 INFO @ Mon, 03 Jun 2019 06:10:41: start model_add_line... INFO @ Mon, 03 Jun 2019 06:10:41: start X-correlation... INFO @ Mon, 03 Jun 2019 06:10:41: end of X-cor INFO @ Mon, 03 Jun 2019 06:10:41: #2 finished! INFO @ Mon, 03 Jun 2019 06:10:41: #2 predicted fragment length is 219 bps INFO @ Mon, 03 Jun 2019 06:10:41: #2 alternative fragment length(s) may be 219 bps INFO @ Mon, 03 Jun 2019 06:10:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.05_model.r INFO @ Mon, 03 Jun 2019 06:10:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:10:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:10:48: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 06:10:48: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 06:10:48: #1 total tags in treatment: 8689595 INFO @ Mon, 03 Jun 2019 06:10:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:10:48: #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 06:10:48: #1 tags after filtering in treatment: 8689595 INFO @ Mon, 03 Jun 2019 06:10:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:10:48: #1 finished! INFO @ Mon, 03 Jun 2019 06:10:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:10:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:10:48: 7000000 INFO @ Mon, 03 Jun 2019 06:10:49: #2 number of paired peaks: 7270 INFO @ Mon, 03 Jun 2019 06:10:49: start model_add_line... INFO @ Mon, 03 Jun 2019 06:10:49: start X-correlation... INFO @ Mon, 03 Jun 2019 06:10:49: end of X-cor INFO @ Mon, 03 Jun 2019 06:10:49: #2 finished! INFO @ Mon, 03 Jun 2019 06:10:49: #2 predicted fragment length is 219 bps INFO @ Mon, 03 Jun 2019 06:10:49: #2 alternative fragment length(s) may be 219 bps INFO @ Mon, 03 Jun 2019 06:10:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.20_model.r INFO @ Mon, 03 Jun 2019 06:10:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:10:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:10:59: 8000000 INFO @ Mon, 03 Jun 2019 06:11:07: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 06:11:07: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 06:11:07: #1 total tags in treatment: 8689595 INFO @ Mon, 03 Jun 2019 06:11:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:11:07: #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 06:11:08: #1 tags after filtering in treatment: 8689595 INFO @ Mon, 03 Jun 2019 06:11:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:11:08: #1 finished! INFO @ Mon, 03 Jun 2019 06:11:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:11:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:11:09: #2 number of paired peaks: 7270 INFO @ Mon, 03 Jun 2019 06:11:09: start model_add_line... INFO @ Mon, 03 Jun 2019 06:11:09: start X-correlation... INFO @ Mon, 03 Jun 2019 06:11:09: end of X-cor INFO @ Mon, 03 Jun 2019 06:11:09: #2 finished! INFO @ Mon, 03 Jun 2019 06:11:09: #2 predicted fragment length is 219 bps INFO @ Mon, 03 Jun 2019 06:11:09: #2 alternative fragment length(s) may be 219 bps INFO @ Mon, 03 Jun 2019 06:11:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.10_model.r INFO @ Mon, 03 Jun 2019 06:11:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:11:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:11:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:11:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:11:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:11:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:11:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.05_summits.bed INFO @ Mon, 03 Jun 2019 06:11:31: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (9966 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:11:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:11:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:11:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.20_summits.bed INFO @ Mon, 03 Jun 2019 06:11:38: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (6544 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 06:11:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:11:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:11:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:11:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201896/SRX201896.10_summits.bed INFO @ Mon, 03 Jun 2019 06:11:59: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8255 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。