Job ID = 1294141 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,006,122 reads read : 11,006,122 reads written : 11,006,122 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: 00:03:00 11006122 reads; of these: 11006122 (100.00%) were unpaired; of these: 624253 (5.67%) aligned 0 times 8745017 (79.46%) aligned exactly 1 time 1636852 (14.87%) aligned >1 times 94.33% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 1853408 / 10381869 = 0.1785 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 05:08:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.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 05:08:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:08:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:08:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.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 05:08:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:08:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:08:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.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 05:08:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:08:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:08:16: 1000000 INFO @ Mon, 03 Jun 2019 05:08:17: 1000000 INFO @ Mon, 03 Jun 2019 05:08:18: 1000000 INFO @ Mon, 03 Jun 2019 05:08:25: 2000000 INFO @ Mon, 03 Jun 2019 05:08:25: 2000000 INFO @ Mon, 03 Jun 2019 05:08:28: 2000000 INFO @ Mon, 03 Jun 2019 05:08:33: 3000000 INFO @ Mon, 03 Jun 2019 05:08:33: 3000000 INFO @ Mon, 03 Jun 2019 05:08:38: 3000000 INFO @ Mon, 03 Jun 2019 05:08:41: 4000000 INFO @ Mon, 03 Jun 2019 05:08:42: 4000000 INFO @ Mon, 03 Jun 2019 05:08:48: 4000000 INFO @ Mon, 03 Jun 2019 05:08:49: 5000000 INFO @ Mon, 03 Jun 2019 05:08:50: 5000000 INFO @ Mon, 03 Jun 2019 05:08:57: 6000000 INFO @ Mon, 03 Jun 2019 05:08:58: 5000000 INFO @ Mon, 03 Jun 2019 05:08:59: 6000000 INFO @ Mon, 03 Jun 2019 05:09:05: 7000000 INFO @ Mon, 03 Jun 2019 05:09:07: 7000000 INFO @ Mon, 03 Jun 2019 05:09:07: 6000000 INFO @ Mon, 03 Jun 2019 05:09:13: 8000000 INFO @ Mon, 03 Jun 2019 05:09:15: 8000000 INFO @ Mon, 03 Jun 2019 05:09:17: 7000000 INFO @ Mon, 03 Jun 2019 05:09:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:09:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:09:18: #1 total tags in treatment: 8528461 INFO @ Mon, 03 Jun 2019 05:09:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:09:18: #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 05:09:18: #1 tags after filtering in treatment: 8528461 INFO @ Mon, 03 Jun 2019 05:09:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:09:18: #1 finished! INFO @ Mon, 03 Jun 2019 05:09:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:09:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:09:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:09:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:09:19: #1 total tags in treatment: 8528461 INFO @ Mon, 03 Jun 2019 05:09:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:09:19: #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 05:09:19: #1 tags after filtering in treatment: 8528461 INFO @ Mon, 03 Jun 2019 05:09:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:09:19: #1 finished! INFO @ Mon, 03 Jun 2019 05:09:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:09:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:09:20: #2 number of paired peaks: 10529 INFO @ Mon, 03 Jun 2019 05:09:20: start model_add_line... INFO @ Mon, 03 Jun 2019 05:09:20: start X-correlation... INFO @ Mon, 03 Jun 2019 05:09:20: end of X-cor INFO @ Mon, 03 Jun 2019 05:09:20: #2 finished! INFO @ Mon, 03 Jun 2019 05:09:20: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 05:09:20: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 05:09:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.10_model.r INFO @ Mon, 03 Jun 2019 05:09:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:09:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:09:21: #2 number of paired peaks: 10529 INFO @ Mon, 03 Jun 2019 05:09:21: start model_add_line... INFO @ Mon, 03 Jun 2019 05:09:21: start X-correlation... INFO @ Mon, 03 Jun 2019 05:09:21: end of X-cor INFO @ Mon, 03 Jun 2019 05:09:21: #2 finished! INFO @ Mon, 03 Jun 2019 05:09:21: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 05:09:21: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 05:09:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.05_model.r INFO @ Mon, 03 Jun 2019 05:09:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:09:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:09:27: 8000000 INFO @ Mon, 03 Jun 2019 05:09:32: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:09:32: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:09:32: #1 total tags in treatment: 8528461 INFO @ Mon, 03 Jun 2019 05:09:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:09:32: #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 05:09:32: #1 tags after filtering in treatment: 8528461 INFO @ Mon, 03 Jun 2019 05:09:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:09:32: #1 finished! INFO @ Mon, 03 Jun 2019 05:09:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:09:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:09:34: #2 number of paired peaks: 10529 INFO @ Mon, 03 Jun 2019 05:09:34: start model_add_line... INFO @ Mon, 03 Jun 2019 05:09:34: start X-correlation... INFO @ Mon, 03 Jun 2019 05:09:34: end of X-cor INFO @ Mon, 03 Jun 2019 05:09:34: #2 finished! INFO @ Mon, 03 Jun 2019 05:09:34: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 05:09:34: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 05:09:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.20_model.r INFO @ Mon, 03 Jun 2019 05:09:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:09:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:09:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:09:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:10:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:10:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:10:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.05_summits.bed INFO @ Mon, 03 Jun 2019 05:10:03: Done! INFO @ Mon, 03 Jun 2019 05:10:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:10:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:10:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.10_summits.bed INFO @ Mon, 03 Jun 2019 05:10:03: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (13699 records, 4 fields): 19 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (10009 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:10:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:10:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:10:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:10:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193319/SRX193319.20_summits.bed INFO @ Mon, 03 Jun 2019 05:10:18: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (5592 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。