Job ID = 1295202 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,853,628 reads read : 24,853,628 reads written : 24,853,628 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: 00:05:51 24853628 reads; of these: 24853628 (100.00%) were unpaired; of these: 1480657 (5.96%) aligned 0 times 22250308 (89.53%) aligned exactly 1 time 1122663 (4.52%) aligned >1 times 94.04% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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] 10003087 / 23372971 = 0.4280 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 13:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.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 13:00:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:00:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.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 13:00:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:00:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.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 13:00:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:00:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:01:03: 1000000 INFO @ Mon, 03 Jun 2019 13:01:03: 1000000 INFO @ Mon, 03 Jun 2019 13:01:03: 1000000 INFO @ Mon, 03 Jun 2019 13:01:11: 2000000 INFO @ Mon, 03 Jun 2019 13:01:12: 2000000 INFO @ Mon, 03 Jun 2019 13:01:12: 2000000 INFO @ Mon, 03 Jun 2019 13:01:20: 3000000 INFO @ Mon, 03 Jun 2019 13:01:20: 3000000 INFO @ Mon, 03 Jun 2019 13:01:21: 3000000 INFO @ Mon, 03 Jun 2019 13:01:28: 4000000 INFO @ Mon, 03 Jun 2019 13:01:29: 4000000 INFO @ Mon, 03 Jun 2019 13:01:30: 4000000 INFO @ Mon, 03 Jun 2019 13:01:37: 5000000 INFO @ Mon, 03 Jun 2019 13:01:38: 5000000 INFO @ Mon, 03 Jun 2019 13:01:40: 5000000 INFO @ Mon, 03 Jun 2019 13:01:45: 6000000 INFO @ Mon, 03 Jun 2019 13:01:47: 6000000 INFO @ Mon, 03 Jun 2019 13:01:48: 6000000 INFO @ Mon, 03 Jun 2019 13:01:55: 7000000 INFO @ Mon, 03 Jun 2019 13:01:56: 7000000 INFO @ Mon, 03 Jun 2019 13:01:57: 7000000 INFO @ Mon, 03 Jun 2019 13:02:03: 8000000 INFO @ Mon, 03 Jun 2019 13:02:05: 8000000 INFO @ Mon, 03 Jun 2019 13:02:07: 8000000 INFO @ Mon, 03 Jun 2019 13:02:12: 9000000 INFO @ Mon, 03 Jun 2019 13:02:15: 9000000 INFO @ Mon, 03 Jun 2019 13:02:16: 9000000 INFO @ Mon, 03 Jun 2019 13:02:21: 10000000 INFO @ Mon, 03 Jun 2019 13:02:24: 10000000 INFO @ Mon, 03 Jun 2019 13:02:26: 10000000 INFO @ Mon, 03 Jun 2019 13:02:30: 11000000 INFO @ Mon, 03 Jun 2019 13:02:33: 11000000 INFO @ Mon, 03 Jun 2019 13:02:37: 11000000 INFO @ Mon, 03 Jun 2019 13:02:39: 12000000 INFO @ Mon, 03 Jun 2019 13:02:42: 12000000 INFO @ Mon, 03 Jun 2019 13:02:46: 12000000 INFO @ Mon, 03 Jun 2019 13:02:47: 13000000 INFO @ Mon, 03 Jun 2019 13:02:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:02:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:02:51: #1 total tags in treatment: 13369884 INFO @ Mon, 03 Jun 2019 13:02:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:02:51: #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 13:02:51: #1 tags after filtering in treatment: 13369884 INFO @ Mon, 03 Jun 2019 13:02:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:02:51: #1 finished! INFO @ Mon, 03 Jun 2019 13:02:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:02:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:02:51: 13000000 INFO @ Mon, 03 Jun 2019 13:02:54: #2 number of paired peaks: 13088 INFO @ Mon, 03 Jun 2019 13:02:54: start model_add_line... INFO @ Mon, 03 Jun 2019 13:02:54: start X-correlation... INFO @ Mon, 03 Jun 2019 13:02:54: end of X-cor INFO @ Mon, 03 Jun 2019 13:02:54: #2 finished! INFO @ Mon, 03 Jun 2019 13:02:54: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 13:02:54: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 03 Jun 2019 13:02:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.05_model.r INFO @ Mon, 03 Jun 2019 13:02:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:02:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:02:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:02:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:02:55: #1 total tags in treatment: 13369884 INFO @ Mon, 03 Jun 2019 13:02:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:02:55: #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 13:02:55: #1 tags after filtering in treatment: 13369884 INFO @ Mon, 03 Jun 2019 13:02:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:02:55: #1 finished! INFO @ Mon, 03 Jun 2019 13:02:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:02:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:02:55: 13000000 INFO @ Mon, 03 Jun 2019 13:02:58: #2 number of paired peaks: 13088 INFO @ Mon, 03 Jun 2019 13:02:58: start model_add_line... INFO @ Mon, 03 Jun 2019 13:02:58: start X-correlation... INFO @ Mon, 03 Jun 2019 13:02:58: end of X-cor INFO @ Mon, 03 Jun 2019 13:02:58: #2 finished! INFO @ Mon, 03 Jun 2019 13:02:58: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 13:02:58: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 03 Jun 2019 13:02:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.10_model.r INFO @ Mon, 03 Jun 2019 13:02:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:02:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:02:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:02:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:02:59: #1 total tags in treatment: 13369884 INFO @ Mon, 03 Jun 2019 13:02:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:02:59: #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 13:02:59: #1 tags after filtering in treatment: 13369884 INFO @ Mon, 03 Jun 2019 13:02:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:02:59: #1 finished! INFO @ Mon, 03 Jun 2019 13:02:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:02:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:03:02: #2 number of paired peaks: 13088 INFO @ Mon, 03 Jun 2019 13:03:02: start model_add_line... INFO @ Mon, 03 Jun 2019 13:03:02: start X-correlation... INFO @ Mon, 03 Jun 2019 13:03:02: end of X-cor INFO @ Mon, 03 Jun 2019 13:03:02: #2 finished! INFO @ Mon, 03 Jun 2019 13:03:02: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 13:03:02: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 03 Jun 2019 13:03:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.20_model.r INFO @ Mon, 03 Jun 2019 13:03:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:03:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:03:48: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 13:03:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:03:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:04:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:04:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:04:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.05_summits.bed INFO @ Mon, 03 Jun 2019 13:04:05: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7544 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:04:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:04:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:04:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.10_summits.bed INFO @ Mon, 03 Jun 2019 13:04:11: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7277 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:04:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:04:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:04:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331384/SRX331384.20_summits.bed INFO @ Mon, 03 Jun 2019 13:04:13: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6906 records, 4 fields): 30 millis CompletedMACS2peakCalling BigWig に変換しました。