Job ID = 2002143 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,382,149 reads read : 19,382,149 reads written : 19,382,149 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: 00:08:04 19382149 reads; of these: 19382149 (100.00%) were unpaired; of these: 533565 (2.75%) aligned 0 times 14344561 (74.01%) aligned exactly 1 time 4504023 (23.24%) aligned >1 times 97.25% overall alignment rate Time searching: 00:08:05 Overall time: 00:08:05 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] 1326880 / 18848584 = 0.0704 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 @ Fri, 05 Jul 2019 10:40:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.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 @ Fri, 05 Jul 2019 10:40:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:40:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:40:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.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 @ Fri, 05 Jul 2019 10:40:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:40:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:40:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.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 @ Fri, 05 Jul 2019 10:40:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:40:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:40:22: 1000000 INFO @ Fri, 05 Jul 2019 10:40:24: 1000000 INFO @ Fri, 05 Jul 2019 10:40:24: 1000000 INFO @ Fri, 05 Jul 2019 10:40:29: 2000000 INFO @ Fri, 05 Jul 2019 10:40:30: 2000000 INFO @ Fri, 05 Jul 2019 10:40:31: 2000000 INFO @ Fri, 05 Jul 2019 10:40:36: 3000000 INFO @ Fri, 05 Jul 2019 10:40:36: 3000000 INFO @ Fri, 05 Jul 2019 10:40:39: 3000000 INFO @ Fri, 05 Jul 2019 10:40:43: 4000000 INFO @ Fri, 05 Jul 2019 10:40:44: 4000000 INFO @ Fri, 05 Jul 2019 10:40:46: 4000000 INFO @ Fri, 05 Jul 2019 10:40:49: 5000000 INFO @ Fri, 05 Jul 2019 10:40:50: 5000000 INFO @ Fri, 05 Jul 2019 10:40:54: 5000000 INFO @ Fri, 05 Jul 2019 10:40:55: 6000000 INFO @ Fri, 05 Jul 2019 10:40:57: 6000000 INFO @ Fri, 05 Jul 2019 10:41:02: 6000000 INFO @ Fri, 05 Jul 2019 10:41:02: 7000000 INFO @ Fri, 05 Jul 2019 10:41:04: 7000000 INFO @ Fri, 05 Jul 2019 10:41:08: 8000000 INFO @ Fri, 05 Jul 2019 10:41:09: 7000000 INFO @ Fri, 05 Jul 2019 10:41:11: 8000000 INFO @ Fri, 05 Jul 2019 10:41:14: 9000000 INFO @ Fri, 05 Jul 2019 10:41:17: 8000000 INFO @ Fri, 05 Jul 2019 10:41:18: 9000000 INFO @ Fri, 05 Jul 2019 10:41:20: 10000000 INFO @ Fri, 05 Jul 2019 10:41:24: 9000000 INFO @ Fri, 05 Jul 2019 10:41:25: 10000000 INFO @ Fri, 05 Jul 2019 10:41:27: 11000000 INFO @ Fri, 05 Jul 2019 10:41:31: 11000000 INFO @ Fri, 05 Jul 2019 10:41:32: 10000000 INFO @ Fri, 05 Jul 2019 10:41:33: 12000000 INFO @ Fri, 05 Jul 2019 10:41:38: 12000000 INFO @ Fri, 05 Jul 2019 10:41:39: 13000000 INFO @ Fri, 05 Jul 2019 10:41:40: 11000000 INFO @ Fri, 05 Jul 2019 10:41:45: 13000000 INFO @ Fri, 05 Jul 2019 10:41:46: 14000000 INFO @ Fri, 05 Jul 2019 10:41:47: 12000000 INFO @ Fri, 05 Jul 2019 10:41:52: 15000000 INFO @ Fri, 05 Jul 2019 10:41:52: 14000000 INFO @ Fri, 05 Jul 2019 10:41:55: 13000000 INFO @ Fri, 05 Jul 2019 10:41:58: 16000000 INFO @ Fri, 05 Jul 2019 10:41:59: 15000000 INFO @ Fri, 05 Jul 2019 10:42:03: 14000000 INFO @ Fri, 05 Jul 2019 10:42:05: 17000000 INFO @ Fri, 05 Jul 2019 10:42:06: 16000000 INFO @ Fri, 05 Jul 2019 10:42:08: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:42:08: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:42:08: #1 total tags in treatment: 17521704 INFO @ Fri, 05 Jul 2019 10:42:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:42:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:42:09: #1 tags after filtering in treatment: 17521515 INFO @ Fri, 05 Jul 2019 10:42:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:42:09: #1 finished! INFO @ Fri, 05 Jul 2019 10:42:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:42:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:42:10: 15000000 INFO @ Fri, 05 Jul 2019 10:42:13: 17000000 INFO @ Fri, 05 Jul 2019 10:42:14: #2 number of paired peaks: 79005 INFO @ Fri, 05 Jul 2019 10:42:14: start model_add_line... INFO @ Fri, 05 Jul 2019 10:42:14: start X-correlation... INFO @ Fri, 05 Jul 2019 10:42:14: end of X-cor INFO @ Fri, 05 Jul 2019 10:42:14: #2 finished! INFO @ Fri, 05 Jul 2019 10:42:14: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 10:42:14: #2 alternative fragment length(s) may be 134,505 bps INFO @ Fri, 05 Jul 2019 10:42:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.20_model.r INFO @ Fri, 05 Jul 2019 10:42:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:42:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:42:17: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:42:17: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:42:17: #1 total tags in treatment: 17521704 INFO @ Fri, 05 Jul 2019 10:42:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:42:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:42:17: #1 tags after filtering in treatment: 17521515 INFO @ Fri, 05 Jul 2019 10:42:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:42:17: #1 finished! INFO @ Fri, 05 Jul 2019 10:42:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:42:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:42:18: 16000000 INFO @ Fri, 05 Jul 2019 10:42:22: #2 number of paired peaks: 79005 INFO @ Fri, 05 Jul 2019 10:42:22: start model_add_line... INFO @ Fri, 05 Jul 2019 10:42:23: start X-correlation... INFO @ Fri, 05 Jul 2019 10:42:23: end of X-cor INFO @ Fri, 05 Jul 2019 10:42:23: #2 finished! INFO @ Fri, 05 Jul 2019 10:42:23: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 10:42:23: #2 alternative fragment length(s) may be 134,505 bps INFO @ Fri, 05 Jul 2019 10:42:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.05_model.r INFO @ Fri, 05 Jul 2019 10:42:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:42:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:42:25: 17000000 INFO @ Fri, 05 Jul 2019 10:42:30: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:42:30: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:42:30: #1 total tags in treatment: 17521704 INFO @ Fri, 05 Jul 2019 10:42:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:42:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:42:30: #1 tags after filtering in treatment: 17521515 INFO @ Fri, 05 Jul 2019 10:42:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:42:30: #1 finished! INFO @ Fri, 05 Jul 2019 10:42:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:42:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:42:35: #2 number of paired peaks: 79005 INFO @ Fri, 05 Jul 2019 10:42:35: start model_add_line... INFO @ Fri, 05 Jul 2019 10:42:35: start X-correlation... INFO @ Fri, 05 Jul 2019 10:42:35: end of X-cor INFO @ Fri, 05 Jul 2019 10:42:35: #2 finished! INFO @ Fri, 05 Jul 2019 10:42:35: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 10:42:35: #2 alternative fragment length(s) may be 134,505 bps INFO @ Fri, 05 Jul 2019 10:42:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.10_model.r INFO @ Fri, 05 Jul 2019 10:42:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:42:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:43:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:43:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:43:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:43:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.20_peaks.xls INFO @ Fri, 05 Jul 2019 10:43:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:43:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.20_summits.bed INFO @ Fri, 05 Jul 2019 10:43:37: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:43:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:43:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:43:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.05_summits.bed INFO @ Fri, 05 Jul 2019 10:43:47: Done! pass1 - making usageList (69 chroms): 4 millis pass2 - checking and writing primary data (6640 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:43:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:43:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:43:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102043/ERX102043.10_summits.bed INFO @ Fri, 05 Jul 2019 10:43:59: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (1660 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。