Job ID = 1294109 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,064,107 reads read : 12,064,107 reads written : 12,064,107 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: 00:04:32 12064107 reads; of these: 12064107 (100.00%) were unpaired; of these: 437086 (3.62%) aligned 0 times 7004722 (58.06%) aligned exactly 1 time 4622299 (38.31%) aligned >1 times 96.38% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 3067267 / 11627021 = 0.2638 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 05:00:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.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 05:00:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:00:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:00:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.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 05:00:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:00:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:00:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.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 05:00:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:00:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:00:14: 1000000 INFO @ Mon, 03 Jun 2019 05:00:14: 1000000 INFO @ Mon, 03 Jun 2019 05:00:15: 1000000 INFO @ Mon, 03 Jun 2019 05:00:22: 2000000 INFO @ Mon, 03 Jun 2019 05:00:23: 2000000 INFO @ Mon, 03 Jun 2019 05:00:25: 2000000 INFO @ Mon, 03 Jun 2019 05:00:31: 3000000 INFO @ Mon, 03 Jun 2019 05:00:32: 3000000 INFO @ Mon, 03 Jun 2019 05:00:35: 3000000 INFO @ Mon, 03 Jun 2019 05:00:40: 4000000 INFO @ Mon, 03 Jun 2019 05:00:41: 4000000 INFO @ Mon, 03 Jun 2019 05:00:45: 4000000 INFO @ Mon, 03 Jun 2019 05:00:48: 5000000 INFO @ Mon, 03 Jun 2019 05:00:50: 5000000 INFO @ Mon, 03 Jun 2019 05:00:54: 5000000 INFO @ Mon, 03 Jun 2019 05:00:57: 6000000 INFO @ Mon, 03 Jun 2019 05:00:59: 6000000 INFO @ Mon, 03 Jun 2019 05:01:04: 6000000 INFO @ Mon, 03 Jun 2019 05:01:06: 7000000 INFO @ Mon, 03 Jun 2019 05:01:08: 7000000 INFO @ Mon, 03 Jun 2019 05:01:13: 7000000 INFO @ Mon, 03 Jun 2019 05:01:14: 8000000 INFO @ Mon, 03 Jun 2019 05:01:17: 8000000 INFO @ Mon, 03 Jun 2019 05:01:19: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:01:19: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:01:19: #1 total tags in treatment: 8559754 INFO @ Mon, 03 Jun 2019 05:01:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:01:19: #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 05:01:19: #1 tags after filtering in treatment: 8559754 INFO @ Mon, 03 Jun 2019 05:01:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:01:19: #1 finished! INFO @ Mon, 03 Jun 2019 05:01:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:01:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:01:20: #2 number of paired peaks: 1251 INFO @ Mon, 03 Jun 2019 05:01:20: start model_add_line... INFO @ Mon, 03 Jun 2019 05:01:20: start X-correlation... INFO @ Mon, 03 Jun 2019 05:01:20: end of X-cor INFO @ Mon, 03 Jun 2019 05:01:20: #2 finished! INFO @ Mon, 03 Jun 2019 05:01:20: #2 predicted fragment length is 78 bps INFO @ Mon, 03 Jun 2019 05:01:20: #2 alternative fragment length(s) may be 78 bps INFO @ Mon, 03 Jun 2019 05:01:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.10_model.r INFO @ Mon, 03 Jun 2019 05:01:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:01:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:01:22: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:01:22: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:01:22: #1 total tags in treatment: 8559754 INFO @ Mon, 03 Jun 2019 05:01:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:01:22: #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 05:01:22: #1 tags after filtering in treatment: 8559754 INFO @ Mon, 03 Jun 2019 05:01:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:01:22: #1 finished! INFO @ Mon, 03 Jun 2019 05:01:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:01:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:01:23: 8000000 INFO @ Mon, 03 Jun 2019 05:01:23: #2 number of paired peaks: 1251 INFO @ Mon, 03 Jun 2019 05:01:23: start model_add_line... INFO @ Mon, 03 Jun 2019 05:01:23: start X-correlation... INFO @ Mon, 03 Jun 2019 05:01:23: end of X-cor INFO @ Mon, 03 Jun 2019 05:01:23: #2 finished! INFO @ Mon, 03 Jun 2019 05:01:23: #2 predicted fragment length is 78 bps INFO @ Mon, 03 Jun 2019 05:01:23: #2 alternative fragment length(s) may be 78 bps INFO @ Mon, 03 Jun 2019 05:01:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.05_model.r INFO @ Mon, 03 Jun 2019 05:01:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:01:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:01:28: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:01:28: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:01:28: #1 total tags in treatment: 8559754 INFO @ Mon, 03 Jun 2019 05:01:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:01:28: #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 05:01:28: #1 tags after filtering in treatment: 8559754 INFO @ Mon, 03 Jun 2019 05:01:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:01:28: #1 finished! INFO @ Mon, 03 Jun 2019 05:01:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:01:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:01:29: #2 number of paired peaks: 1251 INFO @ Mon, 03 Jun 2019 05:01:29: start model_add_line... INFO @ Mon, 03 Jun 2019 05:01:29: start X-correlation... INFO @ Mon, 03 Jun 2019 05:01:29: end of X-cor INFO @ Mon, 03 Jun 2019 05:01:29: #2 finished! INFO @ Mon, 03 Jun 2019 05:01:29: #2 predicted fragment length is 78 bps INFO @ Mon, 03 Jun 2019 05:01:29: #2 alternative fragment length(s) may be 78 bps INFO @ Mon, 03 Jun 2019 05:01:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.20_model.r INFO @ Mon, 03 Jun 2019 05:01:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:01:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:01:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:01:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:01:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:01:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:01:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.10_summits.bed INFO @ Mon, 03 Jun 2019 05:01:59: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4379 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:02:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:02:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:02:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.05_summits.bed INFO @ Mon, 03 Jun 2019 05:02:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11015 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:02:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:02:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:02:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX187079/SRX187079.20_summits.bed INFO @ Mon, 03 Jun 2019 05:02:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1352 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。