Job ID = 1295115 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,473,698 reads read : 14,473,698 reads written : 14,473,698 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: 00:03:07 14473698 reads; of these: 14473698 (100.00%) were unpaired; of these: 2608932 (18.03%) aligned 0 times 10594156 (73.20%) aligned exactly 1 time 1270610 (8.78%) aligned >1 times 81.97% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 1837874 / 11864766 = 0.1549 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 12:06:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.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 12:06:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:06:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:06:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.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 12:06:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:06:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:06:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.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 12:06:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:06:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:07:03: 1000000 INFO @ Mon, 03 Jun 2019 12:07:05: 1000000 INFO @ Mon, 03 Jun 2019 12:07:05: 1000000 INFO @ Mon, 03 Jun 2019 12:07:10: 2000000 INFO @ Mon, 03 Jun 2019 12:07:13: 2000000 INFO @ Mon, 03 Jun 2019 12:07:13: 2000000 INFO @ Mon, 03 Jun 2019 12:07:17: 3000000 INFO @ Mon, 03 Jun 2019 12:07:21: 3000000 INFO @ Mon, 03 Jun 2019 12:07:21: 3000000 INFO @ Mon, 03 Jun 2019 12:07:24: 4000000 INFO @ Mon, 03 Jun 2019 12:07:30: 4000000 INFO @ Mon, 03 Jun 2019 12:07:30: 4000000 INFO @ Mon, 03 Jun 2019 12:07:30: 5000000 INFO @ Mon, 03 Jun 2019 12:07:37: 6000000 INFO @ Mon, 03 Jun 2019 12:07:38: 5000000 INFO @ Mon, 03 Jun 2019 12:07:38: 5000000 INFO @ Mon, 03 Jun 2019 12:07:44: 7000000 INFO @ Mon, 03 Jun 2019 12:07:46: 6000000 INFO @ Mon, 03 Jun 2019 12:07:46: 6000000 INFO @ Mon, 03 Jun 2019 12:07:51: 8000000 INFO @ Mon, 03 Jun 2019 12:07:54: 7000000 INFO @ Mon, 03 Jun 2019 12:07:54: 7000000 INFO @ Mon, 03 Jun 2019 12:07:58: 9000000 INFO @ Mon, 03 Jun 2019 12:08:03: 8000000 INFO @ Mon, 03 Jun 2019 12:08:03: 8000000 INFO @ Mon, 03 Jun 2019 12:08:05: 10000000 INFO @ Mon, 03 Jun 2019 12:08:06: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 12:08:06: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 12:08:06: #1 total tags in treatment: 10026892 INFO @ Mon, 03 Jun 2019 12:08:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:08:06: #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 12:08:06: #1 tags after filtering in treatment: 10026892 INFO @ Mon, 03 Jun 2019 12:08:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:08:06: #1 finished! INFO @ Mon, 03 Jun 2019 12:08:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:08:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:08:07: #2 number of paired peaks: 659 WARNING @ Mon, 03 Jun 2019 12:08:07: Fewer paired peaks (659) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 659 pairs to build model! INFO @ Mon, 03 Jun 2019 12:08:07: start model_add_line... INFO @ Mon, 03 Jun 2019 12:08:07: start X-correlation... INFO @ Mon, 03 Jun 2019 12:08:07: end of X-cor INFO @ Mon, 03 Jun 2019 12:08:07: #2 finished! INFO @ Mon, 03 Jun 2019 12:08:07: #2 predicted fragment length is 270 bps INFO @ Mon, 03 Jun 2019 12:08:07: #2 alternative fragment length(s) may be 270 bps INFO @ Mon, 03 Jun 2019 12:08:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.05_model.r INFO @ Mon, 03 Jun 2019 12:08:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:08:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:08:11: 9000000 INFO @ Mon, 03 Jun 2019 12:08:11: 9000000 INFO @ Mon, 03 Jun 2019 12:08:19: 10000000 INFO @ Mon, 03 Jun 2019 12:08:19: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 12:08:19: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 12:08:19: #1 total tags in treatment: 10026892 INFO @ Mon, 03 Jun 2019 12:08:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:08:19: #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 12:08:19: 10000000 INFO @ Mon, 03 Jun 2019 12:08:19: #1 tags after filtering in treatment: 10026892 INFO @ Mon, 03 Jun 2019 12:08:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:08:19: #1 finished! INFO @ Mon, 03 Jun 2019 12:08:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:08:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:08:19: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 12:08:19: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 12:08:19: #1 total tags in treatment: 10026892 INFO @ Mon, 03 Jun 2019 12:08:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:08:19: #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 12:08:19: #1 tags after filtering in treatment: 10026892 INFO @ Mon, 03 Jun 2019 12:08:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:08:19: #1 finished! INFO @ Mon, 03 Jun 2019 12:08:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:08:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:08:20: #2 number of paired peaks: 659 WARNING @ Mon, 03 Jun 2019 12:08:20: Fewer paired peaks (659) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 659 pairs to build model! INFO @ Mon, 03 Jun 2019 12:08:20: start model_add_line... INFO @ Mon, 03 Jun 2019 12:08:20: start X-correlation... INFO @ Mon, 03 Jun 2019 12:08:20: end of X-cor INFO @ Mon, 03 Jun 2019 12:08:20: #2 finished! INFO @ Mon, 03 Jun 2019 12:08:20: #2 predicted fragment length is 270 bps INFO @ Mon, 03 Jun 2019 12:08:20: #2 alternative fragment length(s) may be 270 bps INFO @ Mon, 03 Jun 2019 12:08:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.20_model.r INFO @ Mon, 03 Jun 2019 12:08:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:08:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:08:20: #2 number of paired peaks: 659 WARNING @ Mon, 03 Jun 2019 12:08:20: Fewer paired peaks (659) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 659 pairs to build model! INFO @ Mon, 03 Jun 2019 12:08:20: start model_add_line... INFO @ Mon, 03 Jun 2019 12:08:21: start X-correlation... INFO @ Mon, 03 Jun 2019 12:08:21: end of X-cor INFO @ Mon, 03 Jun 2019 12:08:21: #2 finished! INFO @ Mon, 03 Jun 2019 12:08:21: #2 predicted fragment length is 270 bps INFO @ Mon, 03 Jun 2019 12:08:21: #2 alternative fragment length(s) may be 270 bps INFO @ Mon, 03 Jun 2019 12:08:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.10_model.r INFO @ Mon, 03 Jun 2019 12:08:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:08:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:08:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:08:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:08:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:08:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:08:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:08:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.05_summits.bed INFO @ Mon, 03 Jun 2019 12:08:57: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (11065 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:09:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:09:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:09:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.20_summits.bed INFO @ Mon, 03 Jun 2019 12:09:08: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1782 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:09:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:09:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:09:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX319057/SRX319057.10_summits.bed INFO @ Mon, 03 Jun 2019 12:09:09: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (5862 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。