Job ID = 1294145 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,319,828 reads read : 11,319,828 reads written : 11,319,828 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: 00:02:32 11319828 reads; of these: 11319828 (100.00%) were unpaired; of these: 4729577 (41.78%) aligned 0 times 5366548 (47.41%) aligned exactly 1 time 1223703 (10.81%) aligned >1 times 58.22% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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_rmdupse_core] 2129558 / 6590251 = 0.3231 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 05:07:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.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 05:07:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:07:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:07:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.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 05:07:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:07:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:07:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.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 05:07:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:07:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:07:43: 1000000 INFO @ Mon, 03 Jun 2019 05:07:44: 1000000 INFO @ Mon, 03 Jun 2019 05:07:44: 1000000 INFO @ Mon, 03 Jun 2019 05:07:50: 2000000 INFO @ Mon, 03 Jun 2019 05:07:52: 2000000 INFO @ Mon, 03 Jun 2019 05:07:52: 2000000 INFO @ Mon, 03 Jun 2019 05:07:58: 3000000 INFO @ Mon, 03 Jun 2019 05:08:00: 3000000 INFO @ Mon, 03 Jun 2019 05:08:00: 3000000 INFO @ Mon, 03 Jun 2019 05:08:05: 4000000 INFO @ Mon, 03 Jun 2019 05:08:08: 4000000 INFO @ Mon, 03 Jun 2019 05:08:09: 4000000 INFO @ Mon, 03 Jun 2019 05:08:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:08:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:08:09: #1 total tags in treatment: 4460693 INFO @ Mon, 03 Jun 2019 05:08:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:08:09: #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 05:08:09: #1 tags after filtering in treatment: 4460693 INFO @ Mon, 03 Jun 2019 05:08:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:08:09: #1 finished! INFO @ Mon, 03 Jun 2019 05:08:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:08:10: #2 number of paired peaks: 11694 INFO @ Mon, 03 Jun 2019 05:08:10: start model_add_line... INFO @ Mon, 03 Jun 2019 05:08:10: start X-correlation... INFO @ Mon, 03 Jun 2019 05:08:10: end of X-cor INFO @ Mon, 03 Jun 2019 05:08:10: #2 finished! INFO @ Mon, 03 Jun 2019 05:08:10: #2 predicted fragment length is 241 bps INFO @ Mon, 03 Jun 2019 05:08:10: #2 alternative fragment length(s) may be 241 bps INFO @ Mon, 03 Jun 2019 05:08:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.20_model.r INFO @ Mon, 03 Jun 2019 05:08:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:08:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:08:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:08:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:08:12: #1 total tags in treatment: 4460693 INFO @ Mon, 03 Jun 2019 05:08:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:08:12: #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 05:08:12: #1 tags after filtering in treatment: 4460693 INFO @ Mon, 03 Jun 2019 05:08:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:08:12: #1 finished! INFO @ Mon, 03 Jun 2019 05:08:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:08:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:08:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:08:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:08:12: #1 total tags in treatment: 4460693 INFO @ Mon, 03 Jun 2019 05:08:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:08:12: #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 05:08:12: #1 tags after filtering in treatment: 4460693 INFO @ Mon, 03 Jun 2019 05:08:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:08:12: #1 finished! INFO @ Mon, 03 Jun 2019 05:08:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:08:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:08:13: #2 number of paired peaks: 11694 INFO @ Mon, 03 Jun 2019 05:08:13: start model_add_line... INFO @ Mon, 03 Jun 2019 05:08:13: start X-correlation... INFO @ Mon, 03 Jun 2019 05:08:13: end of X-cor INFO @ Mon, 03 Jun 2019 05:08:13: #2 finished! INFO @ Mon, 03 Jun 2019 05:08:13: #2 predicted fragment length is 241 bps INFO @ Mon, 03 Jun 2019 05:08:13: #2 alternative fragment length(s) may be 241 bps INFO @ Mon, 03 Jun 2019 05:08:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.10_model.r INFO @ Mon, 03 Jun 2019 05:08:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:08:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:08:14: #2 number of paired peaks: 11694 INFO @ Mon, 03 Jun 2019 05:08:14: start model_add_line... INFO @ Mon, 03 Jun 2019 05:08:14: start X-correlation... INFO @ Mon, 03 Jun 2019 05:08:14: end of X-cor INFO @ Mon, 03 Jun 2019 05:08:14: #2 finished! INFO @ Mon, 03 Jun 2019 05:08:14: #2 predicted fragment length is 241 bps INFO @ Mon, 03 Jun 2019 05:08:14: #2 alternative fragment length(s) may be 241 bps INFO @ Mon, 03 Jun 2019 05:08:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.05_model.r INFO @ Mon, 03 Jun 2019 05:08:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:08:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:08:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:08:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:08:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:08:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:08:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:08:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.20_summits.bed INFO @ Mon, 03 Jun 2019 05:08:36: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6355 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:08:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:08:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:08:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.10_summits.bed INFO @ Mon, 03 Jun 2019 05:08:38: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7620 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:08:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:08:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:08:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193323/SRX193323.05_summits.bed INFO @ Mon, 03 Jun 2019 05:08:39: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8394 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。