Job ID = 2640551 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,085,488 reads read : 22,170,976 reads written : 11,085,488 reads 0-length : 11,085,488 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:21 11085488 reads; of these: 11085488 (100.00%) were unpaired; of these: 660422 (5.96%) aligned 0 times 7839848 (70.72%) aligned exactly 1 time 2585218 (23.32%) aligned >1 times 94.04% overall alignment rate Time searching: 00:09:23 Overall time: 00:09:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 484821 / 10425066 = 0.0465 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:48:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:48:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:48:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:48:46: 1000000 INFO @ Sat, 24 Aug 2019 17:48:53: 2000000 INFO @ Sat, 24 Aug 2019 17:49:01: 3000000 INFO @ Sat, 24 Aug 2019 17:49:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:49:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:49:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:49:08: 4000000 INFO @ Sat, 24 Aug 2019 17:49:16: 1000000 INFO @ Sat, 24 Aug 2019 17:49:16: 5000000 INFO @ Sat, 24 Aug 2019 17:49:24: 2000000 INFO @ Sat, 24 Aug 2019 17:49:24: 6000000 INFO @ Sat, 24 Aug 2019 17:49:32: 7000000 INFO @ Sat, 24 Aug 2019 17:49:32: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:49:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:49:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:49:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:49:40: 8000000 INFO @ Sat, 24 Aug 2019 17:49:40: 4000000 INFO @ Sat, 24 Aug 2019 17:49:46: 1000000 INFO @ Sat, 24 Aug 2019 17:49:48: 9000000 INFO @ Sat, 24 Aug 2019 17:49:49: 5000000 INFO @ Sat, 24 Aug 2019 17:49:54: 2000000 INFO @ Sat, 24 Aug 2019 17:49:55: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:49:55: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:49:55: #1 total tags in treatment: 9940245 INFO @ Sat, 24 Aug 2019 17:49:55: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:49:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:49:55: #1 tags after filtering in treatment: 9940033 INFO @ Sat, 24 Aug 2019 17:49:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:49:55: #1 finished! INFO @ Sat, 24 Aug 2019 17:49:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:49:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:49:57: 6000000 INFO @ Sat, 24 Aug 2019 17:49:58: #2 number of paired peaks: 28086 INFO @ Sat, 24 Aug 2019 17:49:58: start model_add_line... INFO @ Sat, 24 Aug 2019 17:49:58: start X-correlation... INFO @ Sat, 24 Aug 2019 17:49:58: end of X-cor INFO @ Sat, 24 Aug 2019 17:49:58: #2 finished! INFO @ Sat, 24 Aug 2019 17:49:58: #2 predicted fragment length is 179 bps INFO @ Sat, 24 Aug 2019 17:49:58: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 24 Aug 2019 17:49:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.05_model.r INFO @ Sat, 24 Aug 2019 17:49:58: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:49:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:50:03: 3000000 INFO @ Sat, 24 Aug 2019 17:50:06: 7000000 INFO @ Sat, 24 Aug 2019 17:50:11: 4000000 INFO @ Sat, 24 Aug 2019 17:50:14: 8000000 INFO @ Sat, 24 Aug 2019 17:50:19: 5000000 INFO @ Sat, 24 Aug 2019 17:50:22: 9000000 INFO @ Sat, 24 Aug 2019 17:50:28: 6000000 INFO @ Sat, 24 Aug 2019 17:50:29: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:50:31: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:50:31: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:50:31: #1 total tags in treatment: 9940245 INFO @ Sat, 24 Aug 2019 17:50:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:50:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:50:31: #1 tags after filtering in treatment: 9940033 INFO @ Sat, 24 Aug 2019 17:50:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:50:31: #1 finished! INFO @ Sat, 24 Aug 2019 17:50:31: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:50:33: #2 number of paired peaks: 28086 INFO @ Sat, 24 Aug 2019 17:50:33: start model_add_line... INFO @ Sat, 24 Aug 2019 17:50:33: start X-correlation... INFO @ Sat, 24 Aug 2019 17:50:33: end of X-cor INFO @ Sat, 24 Aug 2019 17:50:33: #2 finished! INFO @ Sat, 24 Aug 2019 17:50:33: #2 predicted fragment length is 179 bps INFO @ Sat, 24 Aug 2019 17:50:33: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 24 Aug 2019 17:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.10_model.r INFO @ Sat, 24 Aug 2019 17:50:33: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:50:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:50:36: 7000000 INFO @ Sat, 24 Aug 2019 17:50:44: 8000000 INFO @ Sat, 24 Aug 2019 17:50:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:50:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:50:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.05_summits.bed INFO @ Sat, 24 Aug 2019 17:50:45: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (1742 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:50:52: 9000000 INFO @ Sat, 24 Aug 2019 17:51:00: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:51:00: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:51:00: #1 total tags in treatment: 9940245 INFO @ Sat, 24 Aug 2019 17:51:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:51:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:51:01: #1 tags after filtering in treatment: 9940033 INFO @ Sat, 24 Aug 2019 17:51:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:51:01: #1 finished! INFO @ Sat, 24 Aug 2019 17:51:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:51:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:51:03: #2 number of paired peaks: 28086 INFO @ Sat, 24 Aug 2019 17:51:03: start model_add_line... INFO @ Sat, 24 Aug 2019 17:51:03: start X-correlation... INFO @ Sat, 24 Aug 2019 17:51:03: end of X-cor INFO @ Sat, 24 Aug 2019 17:51:03: #2 finished! INFO @ Sat, 24 Aug 2019 17:51:03: #2 predicted fragment length is 179 bps INFO @ Sat, 24 Aug 2019 17:51:03: #2 alternative fragment length(s) may be 179 bps INFO @ Sat, 24 Aug 2019 17:51:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.20_model.r INFO @ Sat, 24 Aug 2019 17:51:03: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:51:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:51:05: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:51:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:51:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:51:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.10_summits.bed INFO @ Sat, 24 Aug 2019 17:51:21: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (395 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:51:35: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:51:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:51:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:51:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375008/SRX5375008.20_summits.bed INFO @ Sat, 24 Aug 2019 17:51:50: Done! pass1 - making usageList (23 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。