Job ID = 1294146 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,323,292 reads read : 6,323,292 reads written : 6,323,292 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: 00:01:58 6323292 reads; of these: 6323292 (100.00%) were unpaired; of these: 217659 (3.44%) aligned 0 times 5017923 (79.36%) aligned exactly 1 time 1087710 (17.20%) aligned >1 times 96.56% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 1298945 / 6105633 = 0.2127 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 05:06:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.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 05:06:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:06:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:06:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.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 05:06:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:06:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:06:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.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 05:06:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:06:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:06:39: 1000000 INFO @ Mon, 03 Jun 2019 05:06:40: 1000000 INFO @ Mon, 03 Jun 2019 05:06:41: 1000000 INFO @ Mon, 03 Jun 2019 05:06:47: 2000000 INFO @ Mon, 03 Jun 2019 05:06:49: 2000000 INFO @ Mon, 03 Jun 2019 05:06:51: 2000000 INFO @ Mon, 03 Jun 2019 05:06:54: 3000000 INFO @ Mon, 03 Jun 2019 05:06:57: 3000000 INFO @ Mon, 03 Jun 2019 05:07:00: 3000000 INFO @ Mon, 03 Jun 2019 05:07:01: 4000000 INFO @ Mon, 03 Jun 2019 05:07:05: 4000000 INFO @ Mon, 03 Jun 2019 05:07:07: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:07:07: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:07:07: #1 total tags in treatment: 4806688 INFO @ Mon, 03 Jun 2019 05:07:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:07:07: #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 05:07:07: #1 tags after filtering in treatment: 4806688 INFO @ Mon, 03 Jun 2019 05:07:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:07:07: #1 finished! INFO @ Mon, 03 Jun 2019 05:07:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:07:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:07:08: #2 number of paired peaks: 10495 INFO @ Mon, 03 Jun 2019 05:07:08: start model_add_line... INFO @ Mon, 03 Jun 2019 05:07:09: start X-correlation... INFO @ Mon, 03 Jun 2019 05:07:09: end of X-cor INFO @ Mon, 03 Jun 2019 05:07:09: #2 finished! INFO @ Mon, 03 Jun 2019 05:07:09: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 05:07:09: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 03 Jun 2019 05:07:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.05_model.r INFO @ Mon, 03 Jun 2019 05:07:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:07:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:07:09: 4000000 INFO @ Mon, 03 Jun 2019 05:07:11: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:07:11: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:07:11: #1 total tags in treatment: 4806688 INFO @ Mon, 03 Jun 2019 05:07:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:07:11: #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 05:07:11: #1 tags after filtering in treatment: 4806688 INFO @ Mon, 03 Jun 2019 05:07:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:07:11: #1 finished! INFO @ Mon, 03 Jun 2019 05:07:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:07:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:07:12: #2 number of paired peaks: 10495 INFO @ Mon, 03 Jun 2019 05:07:12: start model_add_line... INFO @ Mon, 03 Jun 2019 05:07:12: start X-correlation... INFO @ Mon, 03 Jun 2019 05:07:12: end of X-cor INFO @ Mon, 03 Jun 2019 05:07:12: #2 finished! INFO @ Mon, 03 Jun 2019 05:07:12: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 05:07:12: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 03 Jun 2019 05:07:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.10_model.r INFO @ Mon, 03 Jun 2019 05:07:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:07:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:07:16: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:07:16: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:07:16: #1 total tags in treatment: 4806688 INFO @ Mon, 03 Jun 2019 05:07:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:07:16: #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 05:07:16: #1 tags after filtering in treatment: 4806688 INFO @ Mon, 03 Jun 2019 05:07:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:07:16: #1 finished! INFO @ Mon, 03 Jun 2019 05:07:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:07:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:07:18: #2 number of paired peaks: 10495 INFO @ Mon, 03 Jun 2019 05:07:18: start model_add_line... INFO @ Mon, 03 Jun 2019 05:07:18: start X-correlation... INFO @ Mon, 03 Jun 2019 05:07:18: end of X-cor INFO @ Mon, 03 Jun 2019 05:07:18: #2 finished! INFO @ Mon, 03 Jun 2019 05:07:18: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 05:07:18: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 03 Jun 2019 05:07:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.20_model.r INFO @ Mon, 03 Jun 2019 05:07:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:07:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:07:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:07:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:07:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:07:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:07:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.05_summits.bed INFO @ Mon, 03 Jun 2019 05:07:32: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (9294 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:07:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:07:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:07:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:07:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.10_summits.bed INFO @ Mon, 03 Jun 2019 05:07:36: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8148 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 05:07:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:07:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:07:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193324/SRX193324.20_summits.bed INFO @ Mon, 03 Jun 2019 05:07:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6644 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。