Job ID = 2640694 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,776,570 reads read : 37,553,140 reads written : 18,776,570 reads 0-length : 18,776,570 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: 00:12:26 18776570 reads; of these: 18776570 (100.00%) were unpaired; of these: 2320094 (12.36%) aligned 0 times 13751180 (73.24%) aligned exactly 1 time 2705296 (14.41%) aligned >1 times 87.64% overall alignment rate Time searching: 00:12:28 Overall time: 00:12:28 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] 1107470 / 16456476 = 0.0673 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:36:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.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 18:36:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:36:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:37:00: 1000000 INFO @ Sat, 24 Aug 2019 18:37:09: 2000000 INFO @ Sat, 24 Aug 2019 18:37:19: 3000000 INFO @ Sat, 24 Aug 2019 18:37:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.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 18:37:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:37:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:37:28: 4000000 INFO @ Sat, 24 Aug 2019 18:37:31: 1000000 INFO @ Sat, 24 Aug 2019 18:37:38: 5000000 INFO @ Sat, 24 Aug 2019 18:37:43: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:37:49: 6000000 INFO @ Sat, 24 Aug 2019 18:37:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.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 18:37:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:37:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:37:53: 3000000 INFO @ Sat, 24 Aug 2019 18:37:58: 1000000 INFO @ Sat, 24 Aug 2019 18:38:00: 7000000 INFO @ Sat, 24 Aug 2019 18:38:02: 4000000 INFO @ Sat, 24 Aug 2019 18:38:06: 2000000 INFO @ Sat, 24 Aug 2019 18:38:09: 8000000 INFO @ Sat, 24 Aug 2019 18:38:12: 5000000 INFO @ Sat, 24 Aug 2019 18:38:14: 3000000 INFO @ Sat, 24 Aug 2019 18:38:16: 9000000 INFO @ Sat, 24 Aug 2019 18:38:22: 6000000 INFO @ Sat, 24 Aug 2019 18:38:23: 4000000 INFO @ Sat, 24 Aug 2019 18:38:24: 10000000 INFO @ Sat, 24 Aug 2019 18:38:31: 5000000 INFO @ Sat, 24 Aug 2019 18:38:31: 7000000 INFO @ Sat, 24 Aug 2019 18:38:33: 11000000 INFO @ Sat, 24 Aug 2019 18:38:39: 6000000 INFO @ Sat, 24 Aug 2019 18:38:41: 8000000 INFO @ Sat, 24 Aug 2019 18:38:43: 12000000 INFO @ Sat, 24 Aug 2019 18:38:47: 7000000 INFO @ Sat, 24 Aug 2019 18:38:51: 9000000 INFO @ Sat, 24 Aug 2019 18:38:51: 13000000 INFO @ Sat, 24 Aug 2019 18:38:55: 8000000 INFO @ Sat, 24 Aug 2019 18:38:58: 14000000 INFO @ Sat, 24 Aug 2019 18:39:01: 10000000 INFO @ Sat, 24 Aug 2019 18:39:03: 9000000 INFO @ Sat, 24 Aug 2019 18:39:06: 15000000 INFO @ Sat, 24 Aug 2019 18:39:09: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:39:09: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:39:09: #1 total tags in treatment: 15349006 INFO @ Sat, 24 Aug 2019 18:39:09: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:39:09: #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 18:39:09: #1 tags after filtering in treatment: 15348754 INFO @ Sat, 24 Aug 2019 18:39:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:39:09: #1 finished! INFO @ Sat, 24 Aug 2019 18:39:09: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:39:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:39:11: 11000000 INFO @ Sat, 24 Aug 2019 18:39:11: 10000000 INFO @ Sat, 24 Aug 2019 18:39:14: #2 number of paired peaks: 88542 INFO @ Sat, 24 Aug 2019 18:39:14: start model_add_line... INFO @ Sat, 24 Aug 2019 18:39:14: start X-correlation... INFO @ Sat, 24 Aug 2019 18:39:14: end of X-cor INFO @ Sat, 24 Aug 2019 18:39:14: #2 finished! INFO @ Sat, 24 Aug 2019 18:39:14: #2 predicted fragment length is 174 bps INFO @ Sat, 24 Aug 2019 18:39:14: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 24 Aug 2019 18:39:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.05_model.r INFO @ Sat, 24 Aug 2019 18:39:14: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:39:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:39:20: 11000000 INFO @ Sat, 24 Aug 2019 18:39:21: 12000000 INFO @ Sat, 24 Aug 2019 18:39:28: 12000000 INFO @ Sat, 24 Aug 2019 18:39:31: 13000000 INFO @ Sat, 24 Aug 2019 18:39:36: 13000000 INFO @ Sat, 24 Aug 2019 18:39:41: 14000000 INFO @ Sat, 24 Aug 2019 18:39:45: 14000000 INFO @ Sat, 24 Aug 2019 18:39:50: 15000000 INFO @ Sat, 24 Aug 2019 18:39:53: 15000000 INFO @ Sat, 24 Aug 2019 18:39:54: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:39:54: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:39:54: #1 total tags in treatment: 15349006 INFO @ Sat, 24 Aug 2019 18:39:54: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:39:54: #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 18:39:54: #1 tags after filtering in treatment: 15348754 INFO @ Sat, 24 Aug 2019 18:39:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:39:54: #1 finished! INFO @ Sat, 24 Aug 2019 18:39:54: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:39:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:39:56: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:39:56: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:39:56: #1 total tags in treatment: 15349006 INFO @ Sat, 24 Aug 2019 18:39:56: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:39:56: #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 18:39:56: #1 tags after filtering in treatment: 15348754 INFO @ Sat, 24 Aug 2019 18:39:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:39:56: #1 finished! INFO @ Sat, 24 Aug 2019 18:39:56: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:39:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:39:59: #2 number of paired peaks: 88542 INFO @ Sat, 24 Aug 2019 18:39:59: start model_add_line... INFO @ Sat, 24 Aug 2019 18:39:59: start X-correlation... INFO @ Sat, 24 Aug 2019 18:40:00: end of X-cor INFO @ Sat, 24 Aug 2019 18:40:00: #2 finished! INFO @ Sat, 24 Aug 2019 18:40:00: #2 predicted fragment length is 174 bps INFO @ Sat, 24 Aug 2019 18:40:00: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 24 Aug 2019 18:40:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.10_model.r INFO @ Sat, 24 Aug 2019 18:40:00: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:40:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:40:01: #2 number of paired peaks: 88542 INFO @ Sat, 24 Aug 2019 18:40:01: start model_add_line... INFO @ Sat, 24 Aug 2019 18:40:01: start X-correlation... INFO @ Sat, 24 Aug 2019 18:40:01: end of X-cor INFO @ Sat, 24 Aug 2019 18:40:01: #2 finished! INFO @ Sat, 24 Aug 2019 18:40:01: #2 predicted fragment length is 174 bps INFO @ Sat, 24 Aug 2019 18:40:01: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 24 Aug 2019 18:40:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.20_model.r INFO @ Sat, 24 Aug 2019 18:40:01: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:40:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:40:04: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:40:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:40:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:40:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.05_summits.bed INFO @ Sat, 24 Aug 2019 18:40:30: Done! pass1 - making usageList (111 chroms): 10 millis pass2 - checking and writing primary data (33999 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:40:49: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:40:51: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:41:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:41:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:41:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.10_summits.bed INFO @ Sat, 24 Aug 2019 18:41:15: Done! pass1 - making usageList (83 chroms): 8 millis pass2 - checking and writing primary data (19583 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:41:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:41:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:41:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375051/SRX5375051.20_summits.bed INFO @ Sat, 24 Aug 2019 18:41:17: Done! pass1 - making usageList (53 chroms): 5 millis pass2 - checking and writing primary data (7879 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。