Job ID = 1293801 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,596,259 reads read : 12,596,259 reads written : 12,596,259 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: 00:03:14 12596259 reads; of these: 12596259 (100.00%) were unpaired; of these: 941326 (7.47%) aligned 0 times 10476742 (83.17%) aligned exactly 1 time 1178191 (9.35%) aligned >1 times 92.53% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 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] 8824185 / 11654933 = 0.7571 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 02:36:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.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 02:36:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:36:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:36:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.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 02:36:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:36:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:36:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.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 02:36:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:36:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:36:24: 1000000 INFO @ Mon, 03 Jun 2019 02:36:25: 1000000 INFO @ Mon, 03 Jun 2019 02:36:25: 1000000 INFO @ Mon, 03 Jun 2019 02:36:31: 2000000 INFO @ Mon, 03 Jun 2019 02:36:32: 2000000 INFO @ Mon, 03 Jun 2019 02:36:33: 2000000 INFO @ Mon, 03 Jun 2019 02:36:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:36:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:36:38: #1 total tags in treatment: 2830748 INFO @ Mon, 03 Jun 2019 02:36:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:36:38: #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 02:36:38: #1 tags after filtering in treatment: 2830748 INFO @ Mon, 03 Jun 2019 02:36:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:36:38: #1 finished! INFO @ Mon, 03 Jun 2019 02:36:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:36:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:36:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:36:38: #1 total tags in treatment: 2830748 INFO @ Mon, 03 Jun 2019 02:36:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:36:38: #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 02:36:38: #1 tags after filtering in treatment: 2830748 INFO @ Mon, 03 Jun 2019 02:36:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:36:38: #1 finished! INFO @ Mon, 03 Jun 2019 02:36:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:36:38: #2 number of paired peaks: 6622 INFO @ Mon, 03 Jun 2019 02:36:38: start model_add_line... INFO @ Mon, 03 Jun 2019 02:36:38: start X-correlation... INFO @ Mon, 03 Jun 2019 02:36:39: end of X-cor INFO @ Mon, 03 Jun 2019 02:36:39: #2 finished! INFO @ Mon, 03 Jun 2019 02:36:39: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 02:36:39: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 02:36:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.20_model.r INFO @ Mon, 03 Jun 2019 02:36:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:36:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:36:39: #2 number of paired peaks: 6622 INFO @ Mon, 03 Jun 2019 02:36:39: start model_add_line... INFO @ Mon, 03 Jun 2019 02:36:39: start X-correlation... INFO @ Mon, 03 Jun 2019 02:36:39: end of X-cor INFO @ Mon, 03 Jun 2019 02:36:39: #2 finished! INFO @ Mon, 03 Jun 2019 02:36:39: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 02:36:39: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 02:36:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.10_model.r INFO @ Mon, 03 Jun 2019 02:36:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:36:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:36:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:36:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:36:39: #1 total tags in treatment: 2830748 INFO @ Mon, 03 Jun 2019 02:36:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:36:39: #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 02:36:39: #1 tags after filtering in treatment: 2830748 INFO @ Mon, 03 Jun 2019 02:36:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:36:39: #1 finished! INFO @ Mon, 03 Jun 2019 02:36:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:36:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:36:40: #2 number of paired peaks: 6622 INFO @ Mon, 03 Jun 2019 02:36:40: start model_add_line... INFO @ Mon, 03 Jun 2019 02:36:40: start X-correlation... INFO @ Mon, 03 Jun 2019 02:36:40: end of X-cor INFO @ Mon, 03 Jun 2019 02:36:40: #2 finished! INFO @ Mon, 03 Jun 2019 02:36:40: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 02:36:40: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 02:36:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.05_model.r INFO @ Mon, 03 Jun 2019 02:36:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:36:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:36:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:36:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:36:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:36:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:36:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:36:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.10_summits.bed INFO @ Mon, 03 Jun 2019 02:36:56: Done! INFO @ Mon, 03 Jun 2019 02:36:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:36:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:36:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.20_summits.bed pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (4552 records, 4 fields): 13 millis INFO @ Mon, 03 Jun 2019 02:36:56: Done! CompletedMACS2peakCalling pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3109 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:36:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:36:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:36:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134702/SRX1134702.05_summits.bed INFO @ Mon, 03 Jun 2019 02:36:57: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5926 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。