Job ID = 1295201 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,517,323 reads read : 17,517,323 reads written : 17,517,323 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: 00:04:33 17517323 reads; of these: 17517323 (100.00%) were unpaired; of these: 951098 (5.43%) aligned 0 times 15746938 (89.89%) aligned exactly 1 time 819287 (4.68%) aligned >1 times 94.57% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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] 6253062 / 16566225 = 0.3775 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 12:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.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 12:52:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:52:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.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 12:52:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:52:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.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 12:52:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:52:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:52:45: 1000000 INFO @ Mon, 03 Jun 2019 12:52:45: 1000000 INFO @ Mon, 03 Jun 2019 12:52:45: 1000000 INFO @ Mon, 03 Jun 2019 12:52:53: 2000000 INFO @ Mon, 03 Jun 2019 12:52:55: 2000000 INFO @ Mon, 03 Jun 2019 12:52:55: 2000000 INFO @ Mon, 03 Jun 2019 12:53:02: 3000000 INFO @ Mon, 03 Jun 2019 12:53:03: 3000000 INFO @ Mon, 03 Jun 2019 12:53:04: 3000000 INFO @ Mon, 03 Jun 2019 12:53:09: 4000000 INFO @ Mon, 03 Jun 2019 12:53:12: 4000000 INFO @ Mon, 03 Jun 2019 12:53:14: 4000000 INFO @ Mon, 03 Jun 2019 12:53:17: 5000000 INFO @ Mon, 03 Jun 2019 12:53:21: 5000000 INFO @ Mon, 03 Jun 2019 12:53:22: 5000000 INFO @ Mon, 03 Jun 2019 12:53:25: 6000000 INFO @ Mon, 03 Jun 2019 12:53:30: 6000000 INFO @ Mon, 03 Jun 2019 12:53:31: 6000000 INFO @ Mon, 03 Jun 2019 12:53:33: 7000000 INFO @ Mon, 03 Jun 2019 12:53:38: 7000000 INFO @ Mon, 03 Jun 2019 12:53:41: 8000000 INFO @ Mon, 03 Jun 2019 12:53:41: 7000000 INFO @ Mon, 03 Jun 2019 12:53:47: 8000000 INFO @ Mon, 03 Jun 2019 12:53:49: 9000000 INFO @ Mon, 03 Jun 2019 12:53:50: 8000000 INFO @ Mon, 03 Jun 2019 12:53:56: 9000000 INFO @ Mon, 03 Jun 2019 12:53:56: 10000000 INFO @ Mon, 03 Jun 2019 12:53:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:53:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:53:59: #1 total tags in treatment: 10313163 INFO @ Mon, 03 Jun 2019 12:53:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:53:59: #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 12:53:59: #1 tags after filtering in treatment: 10313163 INFO @ Mon, 03 Jun 2019 12:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:53:59: #1 finished! INFO @ Mon, 03 Jun 2019 12:53:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:53:59: 9000000 INFO @ Mon, 03 Jun 2019 12:54:01: #2 number of paired peaks: 12452 INFO @ Mon, 03 Jun 2019 12:54:01: start model_add_line... INFO @ Mon, 03 Jun 2019 12:54:01: start X-correlation... INFO @ Mon, 03 Jun 2019 12:54:01: end of X-cor INFO @ Mon, 03 Jun 2019 12:54:01: #2 finished! INFO @ Mon, 03 Jun 2019 12:54:01: #2 predicted fragment length is 218 bps INFO @ Mon, 03 Jun 2019 12:54:01: #2 alternative fragment length(s) may be 218 bps INFO @ Mon, 03 Jun 2019 12:54:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.20_model.r INFO @ Mon, 03 Jun 2019 12:54:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:54:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:54:05: 10000000 INFO @ Mon, 03 Jun 2019 12:54:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:54:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:54:07: #1 total tags in treatment: 10313163 INFO @ Mon, 03 Jun 2019 12:54:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:54:07: #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 12:54:07: #1 tags after filtering in treatment: 10313163 INFO @ Mon, 03 Jun 2019 12:54:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:54:07: #1 finished! INFO @ Mon, 03 Jun 2019 12:54:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:54:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:54:08: 10000000 INFO @ Mon, 03 Jun 2019 12:54:10: #2 number of paired peaks: 12452 INFO @ Mon, 03 Jun 2019 12:54:10: start model_add_line... INFO @ Mon, 03 Jun 2019 12:54:10: start X-correlation... INFO @ Mon, 03 Jun 2019 12:54:10: end of X-cor INFO @ Mon, 03 Jun 2019 12:54:10: #2 finished! INFO @ Mon, 03 Jun 2019 12:54:10: #2 predicted fragment length is 218 bps INFO @ Mon, 03 Jun 2019 12:54:10: #2 alternative fragment length(s) may be 218 bps INFO @ Mon, 03 Jun 2019 12:54:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.10_model.r INFO @ Mon, 03 Jun 2019 12:54:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:54:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:54:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:54:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:54:11: #1 total tags in treatment: 10313163 INFO @ Mon, 03 Jun 2019 12:54:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:54:11: #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 12:54:11: #1 tags after filtering in treatment: 10313163 INFO @ Mon, 03 Jun 2019 12:54:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:54:11: #1 finished! INFO @ Mon, 03 Jun 2019 12:54:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:54:13: #2 number of paired peaks: 12452 INFO @ Mon, 03 Jun 2019 12:54:13: start model_add_line... INFO @ Mon, 03 Jun 2019 12:54:14: start X-correlation... INFO @ Mon, 03 Jun 2019 12:54:14: end of X-cor INFO @ Mon, 03 Jun 2019 12:54:14: #2 finished! INFO @ Mon, 03 Jun 2019 12:54:14: #2 predicted fragment length is 218 bps INFO @ Mon, 03 Jun 2019 12:54:14: #2 alternative fragment length(s) may be 218 bps INFO @ Mon, 03 Jun 2019 12:54:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.05_model.r INFO @ Mon, 03 Jun 2019 12:54:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:54:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:54:45: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 12:54:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:54:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:54:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:54:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:54:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.20_summits.bed INFO @ Mon, 03 Jun 2019 12:54:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6739 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:55:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:55:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:55:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.10_summits.bed INFO @ Mon, 03 Jun 2019 12:55:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7183 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 12:55:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:55:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:55:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331383/SRX331383.05_summits.bed INFO @ Mon, 03 Jun 2019 12:55:13: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7469 records, 4 fields): 13 millis CompletedMACS2peakCalling