Job ID = 2590274 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,063,648 reads read : 6,063,648 reads written : 6,063,648 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR504796.sra.cache’: 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: 00:01:38 6063648 reads; of these: 6063648 (100.00%) were unpaired; of these: 212197 (3.50%) aligned 0 times 4508856 (74.36%) aligned exactly 1 time 1342595 (22.14%) aligned >1 times 96.50% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 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] 815721 / 5851451 = 0.1394 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 20:24:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.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 20:24:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:24:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:24:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.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 20:24:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:24:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:24:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.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 20:24:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:24:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:25:01: 1000000 INFO @ Mon, 12 Aug 2019 20:25:03: 1000000 INFO @ Mon, 12 Aug 2019 20:25:04: 1000000 INFO @ Mon, 12 Aug 2019 20:25:07: 2000000 INFO @ Mon, 12 Aug 2019 20:25:10: 2000000 INFO @ Mon, 12 Aug 2019 20:25:11: 2000000 INFO @ Mon, 12 Aug 2019 20:25:13: 3000000 INFO @ Mon, 12 Aug 2019 20:25:17: 3000000 INFO @ Mon, 12 Aug 2019 20:25:17: 3000000 INFO @ Mon, 12 Aug 2019 20:25:20: 4000000 INFO @ Mon, 12 Aug 2019 20:25:24: 4000000 INFO @ Mon, 12 Aug 2019 20:25:24: 4000000 INFO @ Mon, 12 Aug 2019 20:25:26: 5000000 INFO @ Mon, 12 Aug 2019 20:25:26: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:25:26: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:25:26: #1 total tags in treatment: 5035730 INFO @ Mon, 12 Aug 2019 20:25:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:25:26: #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 20:25:26: #1 tags after filtering in treatment: 5035730 INFO @ Mon, 12 Aug 2019 20:25:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:25:26: #1 finished! INFO @ Mon, 12 Aug 2019 20:25:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:25:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:25:27: #2 number of paired peaks: 4548 INFO @ Mon, 12 Aug 2019 20:25:27: start model_add_line... INFO @ Mon, 12 Aug 2019 20:25:27: start X-correlation... INFO @ Mon, 12 Aug 2019 20:25:27: end of X-cor INFO @ Mon, 12 Aug 2019 20:25:27: #2 finished! INFO @ Mon, 12 Aug 2019 20:25:27: #2 predicted fragment length is 102 bps INFO @ Mon, 12 Aug 2019 20:25:27: #2 alternative fragment length(s) may be 102 bps INFO @ Mon, 12 Aug 2019 20:25:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.05_model.r INFO @ Mon, 12 Aug 2019 20:25:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:25:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:25:31: 5000000 INFO @ Mon, 12 Aug 2019 20:25:31: 5000000 INFO @ Mon, 12 Aug 2019 20:25:32: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:25:32: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:25:32: #1 total tags in treatment: 5035730 INFO @ Mon, 12 Aug 2019 20:25:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:25:32: #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 20:25:32: #1 tags after filtering in treatment: 5035730 INFO @ Mon, 12 Aug 2019 20:25:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:25:32: #1 finished! INFO @ Mon, 12 Aug 2019 20:25:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:25:32: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:25:32: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:25:32: #1 total tags in treatment: 5035730 INFO @ Mon, 12 Aug 2019 20:25:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:25:32: #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 20:25:32: #1 tags after filtering in treatment: 5035730 INFO @ Mon, 12 Aug 2019 20:25:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:25:32: #1 finished! INFO @ Mon, 12 Aug 2019 20:25:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:25:32: #2 number of paired peaks: 4548 INFO @ Mon, 12 Aug 2019 20:25:32: start model_add_line... INFO @ Mon, 12 Aug 2019 20:25:33: start X-correlation... INFO @ Mon, 12 Aug 2019 20:25:33: end of X-cor INFO @ Mon, 12 Aug 2019 20:25:33: #2 finished! INFO @ Mon, 12 Aug 2019 20:25:33: #2 predicted fragment length is 102 bps INFO @ Mon, 12 Aug 2019 20:25:33: #2 alternative fragment length(s) may be 102 bps INFO @ Mon, 12 Aug 2019 20:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.20_model.r INFO @ Mon, 12 Aug 2019 20:25:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:25:33: #2 number of paired peaks: 4548 INFO @ Mon, 12 Aug 2019 20:25:33: start model_add_line... INFO @ Mon, 12 Aug 2019 20:25:33: start X-correlation... INFO @ Mon, 12 Aug 2019 20:25:33: end of X-cor INFO @ Mon, 12 Aug 2019 20:25:33: #2 finished! INFO @ Mon, 12 Aug 2019 20:25:33: #2 predicted fragment length is 102 bps INFO @ Mon, 12 Aug 2019 20:25:33: #2 alternative fragment length(s) may be 102 bps INFO @ Mon, 12 Aug 2019 20:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.10_model.r INFO @ Mon, 12 Aug 2019 20:25:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:25:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:25:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:25:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:25:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:25:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:25:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.05_summits.bed INFO @ Mon, 12 Aug 2019 20:25:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7922 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:25:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:25:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:25:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.20_summits.bed INFO @ Mon, 12 Aug 2019 20:25:56: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3867 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:25:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:25:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:25:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151962/SRX151962.10_summits.bed INFO @ Mon, 12 Aug 2019 20:25:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6004 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。