Job ID = 2590253 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,650,044 reads read : 35,650,044 reads written : 35,650,044 rm: cannot remove ‘[DSE]RR*’: 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: 00:09:58 35650044 reads; of these: 35650044 (100.00%) were unpaired; of these: 2939548 (8.25%) aligned 0 times 26100272 (73.21%) aligned exactly 1 time 6610224 (18.54%) aligned >1 times 91.75% overall alignment rate Time searching: 00:09:58 Overall time: 00:09:58 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_sort_core] merging from 12 files... [bam_rmdupse_core] 27249351 / 32710496 = 0.8330 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, 12 Aug 2019 20:50:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.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, 12 Aug 2019 20:50:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:50:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:50:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.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, 12 Aug 2019 20:50:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:50:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.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, 12 Aug 2019 20:50:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:50:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:50:23: 1000000 INFO @ Mon, 12 Aug 2019 20:50:23: 1000000 INFO @ Mon, 12 Aug 2019 20:50:25: 1000000 INFO @ Mon, 12 Aug 2019 20:50:31: 2000000 INFO @ Mon, 12 Aug 2019 20:50:31: 2000000 INFO @ Mon, 12 Aug 2019 20:50:34: 2000000 INFO @ Mon, 12 Aug 2019 20:50:38: 3000000 INFO @ Mon, 12 Aug 2019 20:50:39: 3000000 INFO @ Mon, 12 Aug 2019 20:50:42: 3000000 INFO @ Mon, 12 Aug 2019 20:50:45: 4000000 INFO @ Mon, 12 Aug 2019 20:50:48: 4000000 INFO @ Mon, 12 Aug 2019 20:50:51: 4000000 INFO @ Mon, 12 Aug 2019 20:50:52: 5000000 INFO @ Mon, 12 Aug 2019 20:50:55: 5000000 INFO @ Mon, 12 Aug 2019 20:50:55: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:50:55: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:50:55: #1 total tags in treatment: 5461145 INFO @ Mon, 12 Aug 2019 20:50:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:50:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:50:55: #1 tags after filtering in treatment: 5461145 INFO @ Mon, 12 Aug 2019 20:50:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:50:55: #1 finished! INFO @ Mon, 12 Aug 2019 20:50:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:50:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:50:56: #2 number of paired peaks: 2830 INFO @ Mon, 12 Aug 2019 20:50:56: start model_add_line... INFO @ Mon, 12 Aug 2019 20:50:56: start X-correlation... INFO @ Mon, 12 Aug 2019 20:50:56: end of X-cor INFO @ Mon, 12 Aug 2019 20:50:56: #2 finished! INFO @ Mon, 12 Aug 2019 20:50:56: #2 predicted fragment length is 116 bps INFO @ Mon, 12 Aug 2019 20:50:56: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 12 Aug 2019 20:50:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.10_model.r INFO @ Mon, 12 Aug 2019 20:50:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:50:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:50:59: 5000000 INFO @ Mon, 12 Aug 2019 20:50:59: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:50:59: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:50:59: #1 total tags in treatment: 5461145 INFO @ Mon, 12 Aug 2019 20:50:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:50:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:50:59: #1 tags after filtering in treatment: 5461145 INFO @ Mon, 12 Aug 2019 20:50:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:50:59: #1 finished! INFO @ Mon, 12 Aug 2019 20:50:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:50:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:51:00: #2 number of paired peaks: 2830 INFO @ Mon, 12 Aug 2019 20:51:00: start model_add_line... INFO @ Mon, 12 Aug 2019 20:51:00: start X-correlation... INFO @ Mon, 12 Aug 2019 20:51:00: end of X-cor INFO @ Mon, 12 Aug 2019 20:51:00: #2 finished! INFO @ Mon, 12 Aug 2019 20:51:00: #2 predicted fragment length is 116 bps INFO @ Mon, 12 Aug 2019 20:51:00: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 12 Aug 2019 20:51:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.05_model.r INFO @ Mon, 12 Aug 2019 20:51:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:51:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:51:02: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:51:02: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:51:02: #1 total tags in treatment: 5461145 INFO @ Mon, 12 Aug 2019 20:51:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:51:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:51:02: #1 tags after filtering in treatment: 5461145 INFO @ Mon, 12 Aug 2019 20:51:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:51:02: #1 finished! INFO @ Mon, 12 Aug 2019 20:51:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:51:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:51:03: #2 number of paired peaks: 2830 INFO @ Mon, 12 Aug 2019 20:51:03: start model_add_line... INFO @ Mon, 12 Aug 2019 20:51:03: start X-correlation... INFO @ Mon, 12 Aug 2019 20:51:03: end of X-cor INFO @ Mon, 12 Aug 2019 20:51:03: #2 finished! INFO @ Mon, 12 Aug 2019 20:51:03: #2 predicted fragment length is 116 bps INFO @ Mon, 12 Aug 2019 20:51:03: #2 alternative fragment length(s) may be 116 bps INFO @ Mon, 12 Aug 2019 20:51:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.20_model.r INFO @ Mon, 12 Aug 2019 20:51:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:51:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:51:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:51:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:51:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:51:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:51:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.10_summits.bed INFO @ Mon, 12 Aug 2019 20:51:23: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5096 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:51:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:51:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:51:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.05_summits.bed INFO @ Mon, 12 Aug 2019 20:51:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8717 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:51:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2933038/ERX2933038.20_summits.bed INFO @ Mon, 12 Aug 2019 20:51:31: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2900 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。