Job ID = 2590851 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,228,122 reads read : 16,228,122 reads written : 16,228,122 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: 00:05:52 16228122 reads; of these: 16228122 (100.00%) were unpaired; of these: 2748803 (16.94%) aligned 0 times 10206186 (62.89%) aligned exactly 1 time 3273133 (20.17%) aligned >1 times 83.06% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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 8 files... [bam_rmdupse_core] 6234318 / 13479319 = 0.4625 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 23:50:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.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 23:50:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:50:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.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 23:50:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:50:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:50:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.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 23:50:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:50:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:50:16: 1000000 INFO @ Mon, 12 Aug 2019 23:50:17: 1000000 INFO @ Mon, 12 Aug 2019 23:50:18: 1000000 INFO @ Mon, 12 Aug 2019 23:50:22: 2000000 INFO @ Mon, 12 Aug 2019 23:50:23: 2000000 INFO @ Mon, 12 Aug 2019 23:50:25: 2000000 INFO @ Mon, 12 Aug 2019 23:50:29: 3000000 INFO @ Mon, 12 Aug 2019 23:50:30: 3000000 INFO @ Mon, 12 Aug 2019 23:50:32: 3000000 INFO @ Mon, 12 Aug 2019 23:50:35: 4000000 INFO @ Mon, 12 Aug 2019 23:50:36: 4000000 INFO @ Mon, 12 Aug 2019 23:50:39: 4000000 INFO @ Mon, 12 Aug 2019 23:50:41: 5000000 INFO @ Mon, 12 Aug 2019 23:50:42: 5000000 INFO @ Mon, 12 Aug 2019 23:50:46: 5000000 INFO @ Mon, 12 Aug 2019 23:50:48: 6000000 INFO @ Mon, 12 Aug 2019 23:50:48: 6000000 INFO @ Mon, 12 Aug 2019 23:50:52: 6000000 INFO @ Mon, 12 Aug 2019 23:50:54: 7000000 INFO @ Mon, 12 Aug 2019 23:50:55: 7000000 INFO @ Mon, 12 Aug 2019 23:50:55: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:50:55: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:50:55: #1 total tags in treatment: 7245001 INFO @ Mon, 12 Aug 2019 23:50:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:50:55: #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 23:50:56: #1 tags after filtering in treatment: 7245001 INFO @ Mon, 12 Aug 2019 23:50:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:50:56: #1 finished! INFO @ Mon, 12 Aug 2019 23:50:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:50:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:50:56: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:50:56: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:50:56: #1 total tags in treatment: 7245001 INFO @ Mon, 12 Aug 2019 23:50:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:50:56: #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 23:50:57: #2 number of paired peaks: 2964 INFO @ Mon, 12 Aug 2019 23:50:57: start model_add_line... INFO @ Mon, 12 Aug 2019 23:50:57: #1 tags after filtering in treatment: 7245001 INFO @ Mon, 12 Aug 2019 23:50:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:50:57: #1 finished! INFO @ Mon, 12 Aug 2019 23:50:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:50:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:50:57: start X-correlation... INFO @ Mon, 12 Aug 2019 23:50:57: end of X-cor INFO @ Mon, 12 Aug 2019 23:50:57: #2 finished! INFO @ Mon, 12 Aug 2019 23:50:57: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 23:50:57: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 12 Aug 2019 23:50:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.05_model.r INFO @ Mon, 12 Aug 2019 23:50:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:50:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:50:57: #2 number of paired peaks: 2964 INFO @ Mon, 12 Aug 2019 23:50:57: start model_add_line... INFO @ Mon, 12 Aug 2019 23:50:58: start X-correlation... INFO @ Mon, 12 Aug 2019 23:50:58: end of X-cor INFO @ Mon, 12 Aug 2019 23:50:58: #2 finished! INFO @ Mon, 12 Aug 2019 23:50:58: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 23:50:58: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 12 Aug 2019 23:50:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.10_model.r INFO @ Mon, 12 Aug 2019 23:50:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:50:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:50:59: 7000000 INFO @ Mon, 12 Aug 2019 23:51:01: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:51:01: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:51:01: #1 total tags in treatment: 7245001 INFO @ Mon, 12 Aug 2019 23:51:01: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:51:01: #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 23:51:01: #1 tags after filtering in treatment: 7245001 INFO @ Mon, 12 Aug 2019 23:51:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:51:01: #1 finished! INFO @ Mon, 12 Aug 2019 23:51:01: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:51:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:51:02: #2 number of paired peaks: 2964 INFO @ Mon, 12 Aug 2019 23:51:02: start model_add_line... INFO @ Mon, 12 Aug 2019 23:51:02: start X-correlation... INFO @ Mon, 12 Aug 2019 23:51:02: end of X-cor INFO @ Mon, 12 Aug 2019 23:51:02: #2 finished! INFO @ Mon, 12 Aug 2019 23:51:02: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 23:51:02: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 12 Aug 2019 23:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.20_model.r INFO @ Mon, 12 Aug 2019 23:51:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:51:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:24: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.05_summits.bed INFO @ Mon, 12 Aug 2019 23:51:30: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8734 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.10_summits.bed INFO @ Mon, 12 Aug 2019 23:51:31: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5578 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:51:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011085/SRX5011085.20_summits.bed INFO @ Mon, 12 Aug 2019 23:51:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3061 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。