Job ID = 2002142 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,041,346 reads read : 21,041,346 reads written : 21,041,346 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:44 21041346 reads; of these: 21041346 (100.00%) were unpaired; of these: 507024 (2.41%) aligned 0 times 15554936 (73.93%) aligned exactly 1 time 4979386 (23.66%) aligned >1 times 97.59% overall alignment rate Time searching: 00:08:45 Overall time: 00:08:45 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] 1120732 / 20534322 = 0.0546 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 10:37:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.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 10:37:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:37:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:37:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.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 10:37:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:37:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:37:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.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 10:37:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:37:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:37:55: 1000000 INFO @ Fri, 05 Jul 2019 10:37:57: 1000000 INFO @ Fri, 05 Jul 2019 10:37:57: 1000000 INFO @ Fri, 05 Jul 2019 10:38:03: 2000000 INFO @ Fri, 05 Jul 2019 10:38:07: 2000000 INFO @ Fri, 05 Jul 2019 10:38:08: 2000000 INFO @ Fri, 05 Jul 2019 10:38:11: 3000000 INFO @ Fri, 05 Jul 2019 10:38:17: 3000000 INFO @ Fri, 05 Jul 2019 10:38:18: 3000000 INFO @ Fri, 05 Jul 2019 10:38:19: 4000000 INFO @ Fri, 05 Jul 2019 10:38:27: 4000000 INFO @ Fri, 05 Jul 2019 10:38:27: 5000000 INFO @ Fri, 05 Jul 2019 10:38:28: 4000000 INFO @ Fri, 05 Jul 2019 10:38:35: 6000000 INFO @ Fri, 05 Jul 2019 10:38:37: 5000000 INFO @ Fri, 05 Jul 2019 10:38:37: 5000000 INFO @ Fri, 05 Jul 2019 10:38:42: 7000000 INFO @ Fri, 05 Jul 2019 10:38:46: 6000000 INFO @ Fri, 05 Jul 2019 10:38:47: 6000000 INFO @ Fri, 05 Jul 2019 10:38:50: 8000000 INFO @ Fri, 05 Jul 2019 10:38:55: 7000000 INFO @ Fri, 05 Jul 2019 10:38:56: 7000000 INFO @ Fri, 05 Jul 2019 10:38:57: 9000000 INFO @ Fri, 05 Jul 2019 10:39:04: 8000000 INFO @ Fri, 05 Jul 2019 10:39:05: 8000000 INFO @ Fri, 05 Jul 2019 10:39:05: 10000000 INFO @ Fri, 05 Jul 2019 10:39:13: 11000000 INFO @ Fri, 05 Jul 2019 10:39:13: 9000000 INFO @ Fri, 05 Jul 2019 10:39:14: 9000000 INFO @ Fri, 05 Jul 2019 10:39:20: 12000000 INFO @ Fri, 05 Jul 2019 10:39:23: 10000000 INFO @ Fri, 05 Jul 2019 10:39:23: 10000000 INFO @ Fri, 05 Jul 2019 10:39:28: 13000000 INFO @ Fri, 05 Jul 2019 10:39:32: 11000000 INFO @ Fri, 05 Jul 2019 10:39:33: 11000000 INFO @ Fri, 05 Jul 2019 10:39:35: 14000000 INFO @ Fri, 05 Jul 2019 10:39:41: 12000000 INFO @ Fri, 05 Jul 2019 10:39:42: 12000000 INFO @ Fri, 05 Jul 2019 10:39:43: 15000000 INFO @ Fri, 05 Jul 2019 10:39:50: 13000000 INFO @ Fri, 05 Jul 2019 10:39:51: 16000000 INFO @ Fri, 05 Jul 2019 10:39:51: 13000000 INFO @ Fri, 05 Jul 2019 10:39:58: 17000000 INFO @ Fri, 05 Jul 2019 10:40:00: 14000000 INFO @ Fri, 05 Jul 2019 10:40:00: 14000000 INFO @ Fri, 05 Jul 2019 10:40:06: 18000000 INFO @ Fri, 05 Jul 2019 10:40:09: 15000000 INFO @ Fri, 05 Jul 2019 10:40:09: 15000000 INFO @ Fri, 05 Jul 2019 10:40:13: 19000000 INFO @ Fri, 05 Jul 2019 10:40:17: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:40:17: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:40:17: #1 total tags in treatment: 19413590 INFO @ Fri, 05 Jul 2019 10:40:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:40:17: #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 10:40:17: #1 tags after filtering in treatment: 19413412 INFO @ Fri, 05 Jul 2019 10:40:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:40:17: #1 finished! INFO @ Fri, 05 Jul 2019 10:40:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:40:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:40:18: 16000000 INFO @ Fri, 05 Jul 2019 10:40:18: 16000000 INFO @ Fri, 05 Jul 2019 10:40:22: #2 number of paired peaks: 59835 INFO @ Fri, 05 Jul 2019 10:40:22: start model_add_line... INFO @ Fri, 05 Jul 2019 10:40:22: start X-correlation... INFO @ Fri, 05 Jul 2019 10:40:22: end of X-cor INFO @ Fri, 05 Jul 2019 10:40:22: #2 finished! INFO @ Fri, 05 Jul 2019 10:40:22: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 10:40:22: #2 alternative fragment length(s) may be 3,133,503 bps INFO @ Fri, 05 Jul 2019 10:40:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.05_model.r INFO @ Fri, 05 Jul 2019 10:40:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:40:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:40:27: 17000000 INFO @ Fri, 05 Jul 2019 10:40:27: 17000000 INFO @ Fri, 05 Jul 2019 10:40:35: 18000000 INFO @ Fri, 05 Jul 2019 10:40:36: 18000000 INFO @ Fri, 05 Jul 2019 10:40:43: 19000000 INFO @ Fri, 05 Jul 2019 10:40:45: 19000000 INFO @ Fri, 05 Jul 2019 10:40:47: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:40:47: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:40:47: #1 total tags in treatment: 19413590 INFO @ Fri, 05 Jul 2019 10:40:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:40:47: #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 10:40:48: #1 tags after filtering in treatment: 19413412 INFO @ Fri, 05 Jul 2019 10:40:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:40:48: #1 finished! INFO @ Fri, 05 Jul 2019 10:40:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:40:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:40:49: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:40:49: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:40:49: #1 total tags in treatment: 19413590 INFO @ Fri, 05 Jul 2019 10:40:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:40:49: #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 10:40:49: #1 tags after filtering in treatment: 19413412 INFO @ Fri, 05 Jul 2019 10:40:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:40:49: #1 finished! INFO @ Fri, 05 Jul 2019 10:40:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:40:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:40:52: #2 number of paired peaks: 59835 INFO @ Fri, 05 Jul 2019 10:40:52: start model_add_line... INFO @ Fri, 05 Jul 2019 10:40:53: start X-correlation... INFO @ Fri, 05 Jul 2019 10:40:53: end of X-cor INFO @ Fri, 05 Jul 2019 10:40:53: #2 finished! INFO @ Fri, 05 Jul 2019 10:40:53: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 10:40:53: #2 alternative fragment length(s) may be 3,133,503 bps INFO @ Fri, 05 Jul 2019 10:40:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.10_model.r INFO @ Fri, 05 Jul 2019 10:40:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:40:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:40:54: #2 number of paired peaks: 59835 INFO @ Fri, 05 Jul 2019 10:40:54: start model_add_line... INFO @ Fri, 05 Jul 2019 10:40:54: start X-correlation... INFO @ Fri, 05 Jul 2019 10:40:54: end of X-cor INFO @ Fri, 05 Jul 2019 10:40:54: #2 finished! INFO @ Fri, 05 Jul 2019 10:40:54: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 10:40:54: #2 alternative fragment length(s) may be 3,133,503 bps INFO @ Fri, 05 Jul 2019 10:40:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.20_model.r INFO @ Fri, 05 Jul 2019 10:40:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:40:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:41:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:41:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:41:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:41:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.05_summits.bed INFO @ Fri, 05 Jul 2019 10:41:53: Done! pass1 - making usageList (55 chroms): 3 millis pass2 - checking and writing primary data (3359 records, 4 fields): 12 millis INFO @ Fri, 05 Jul 2019 10:41:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:41:55: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:42:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:42:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:42:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.10_summits.bed INFO @ Fri, 05 Jul 2019 10:42:23: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (684 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:42:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.20_peaks.xls INFO @ Fri, 05 Jul 2019 10:42:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:42:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102042/ERX102042.20_summits.bed INFO @ Fri, 05 Jul 2019 10:42:25: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。