Job ID = 2001672 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,660,229 reads read : 21,660,229 reads written : 21,660,229 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:41 21660229 reads; of these: 21660229 (100.00%) were unpaired; of these: 475395 (2.19%) aligned 0 times 16051587 (74.11%) aligned exactly 1 time 5133247 (23.70%) aligned >1 times 97.81% overall alignment rate Time searching: 00:08:44 Overall time: 00:08:44 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] 1200917 / 21184834 = 0.0567 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 08:14:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.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 08:14:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:14:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.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 08:14:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:14:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:14:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.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 08:14:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:14:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:14:42: 1000000 INFO @ Fri, 05 Jul 2019 08:14:43: 1000000 INFO @ Fri, 05 Jul 2019 08:14:44: 1000000 INFO @ Fri, 05 Jul 2019 08:14:51: 2000000 INFO @ Fri, 05 Jul 2019 08:14:52: 2000000 INFO @ Fri, 05 Jul 2019 08:14:53: 2000000 INFO @ Fri, 05 Jul 2019 08:14:59: 3000000 INFO @ Fri, 05 Jul 2019 08:15:00: 3000000 INFO @ Fri, 05 Jul 2019 08:15:02: 3000000 INFO @ Fri, 05 Jul 2019 08:15:07: 4000000 INFO @ Fri, 05 Jul 2019 08:15:09: 4000000 INFO @ Fri, 05 Jul 2019 08:15:11: 4000000 INFO @ Fri, 05 Jul 2019 08:15:15: 5000000 INFO @ Fri, 05 Jul 2019 08:15:18: 5000000 INFO @ Fri, 05 Jul 2019 08:15:21: 5000000 INFO @ Fri, 05 Jul 2019 08:15:25: 6000000 INFO @ Fri, 05 Jul 2019 08:15:27: 6000000 INFO @ Fri, 05 Jul 2019 08:15:30: 6000000 INFO @ Fri, 05 Jul 2019 08:15:33: 7000000 INFO @ Fri, 05 Jul 2019 08:15:35: 7000000 INFO @ Fri, 05 Jul 2019 08:15:39: 7000000 INFO @ Fri, 05 Jul 2019 08:15:42: 8000000 INFO @ Fri, 05 Jul 2019 08:15:44: 8000000 INFO @ Fri, 05 Jul 2019 08:15:47: 8000000 INFO @ Fri, 05 Jul 2019 08:15:51: 9000000 INFO @ Fri, 05 Jul 2019 08:15:53: 9000000 INFO @ Fri, 05 Jul 2019 08:15:56: 9000000 INFO @ Fri, 05 Jul 2019 08:16:00: 10000000 INFO @ Fri, 05 Jul 2019 08:16:01: 10000000 INFO @ Fri, 05 Jul 2019 08:16:05: 10000000 INFO @ Fri, 05 Jul 2019 08:16:08: 11000000 INFO @ Fri, 05 Jul 2019 08:16:09: 11000000 INFO @ Fri, 05 Jul 2019 08:16:13: 11000000 INFO @ Fri, 05 Jul 2019 08:16:17: 12000000 INFO @ Fri, 05 Jul 2019 08:16:18: 12000000 INFO @ Fri, 05 Jul 2019 08:16:22: 12000000 INFO @ Fri, 05 Jul 2019 08:16:26: 13000000 INFO @ Fri, 05 Jul 2019 08:16:26: 13000000 INFO @ Fri, 05 Jul 2019 08:16:30: 13000000 INFO @ Fri, 05 Jul 2019 08:16:35: 14000000 INFO @ Fri, 05 Jul 2019 08:16:35: 14000000 INFO @ Fri, 05 Jul 2019 08:16:39: 14000000 INFO @ Fri, 05 Jul 2019 08:16:43: 15000000 INFO @ Fri, 05 Jul 2019 08:16:43: 15000000 INFO @ Fri, 05 Jul 2019 08:16:48: 15000000 INFO @ Fri, 05 Jul 2019 08:16:52: 16000000 INFO @ Fri, 05 Jul 2019 08:16:52: 16000000 INFO @ Fri, 05 Jul 2019 08:16:56: 16000000 INFO @ Fri, 05 Jul 2019 08:17:00: 17000000 INFO @ Fri, 05 Jul 2019 08:17:01: 17000000 INFO @ Fri, 05 Jul 2019 08:17:04: 17000000 INFO @ Fri, 05 Jul 2019 08:17:09: 18000000 INFO @ Fri, 05 Jul 2019 08:17:10: 18000000 INFO @ Fri, 05 Jul 2019 08:17:13: 18000000 INFO @ Fri, 05 Jul 2019 08:17:17: 19000000 INFO @ Fri, 05 Jul 2019 08:17:20: 19000000 INFO @ Fri, 05 Jul 2019 08:17:24: 19000000 INFO @ Fri, 05 Jul 2019 08:17:26: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:17:26: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:17:26: #1 total tags in treatment: 19983917 INFO @ Fri, 05 Jul 2019 08:17:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:17:26: #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 08:17:26: #1 tags after filtering in treatment: 19983736 INFO @ Fri, 05 Jul 2019 08:17:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:17:26: #1 finished! INFO @ Fri, 05 Jul 2019 08:17:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:17:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:17:30: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:17:30: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:17:30: #1 total tags in treatment: 19983917 INFO @ Fri, 05 Jul 2019 08:17:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:17:30: #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 08:17:31: #2 number of paired peaks: 56584 INFO @ Fri, 05 Jul 2019 08:17:31: start model_add_line... INFO @ Fri, 05 Jul 2019 08:17:31: #1 tags after filtering in treatment: 19983736 INFO @ Fri, 05 Jul 2019 08:17:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:17:31: #1 finished! INFO @ Fri, 05 Jul 2019 08:17:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:17:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:17:31: start X-correlation... INFO @ Fri, 05 Jul 2019 08:17:31: end of X-cor INFO @ Fri, 05 Jul 2019 08:17:31: #2 finished! INFO @ Fri, 05 Jul 2019 08:17:31: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 08:17:31: #2 alternative fragment length(s) may be 4,129 bps INFO @ Fri, 05 Jul 2019 08:17:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.20_model.r INFO @ Fri, 05 Jul 2019 08:17:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:17:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:17:33: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:17:33: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:17:33: #1 total tags in treatment: 19983917 INFO @ Fri, 05 Jul 2019 08:17:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:17:33: #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 08:17:34: #1 tags after filtering in treatment: 19983736 INFO @ Fri, 05 Jul 2019 08:17:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:17:34: #1 finished! INFO @ Fri, 05 Jul 2019 08:17:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:17:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:17:35: #2 number of paired peaks: 56584 INFO @ Fri, 05 Jul 2019 08:17:35: start model_add_line... INFO @ Fri, 05 Jul 2019 08:17:36: start X-correlation... INFO @ Fri, 05 Jul 2019 08:17:36: end of X-cor INFO @ Fri, 05 Jul 2019 08:17:36: #2 finished! INFO @ Fri, 05 Jul 2019 08:17:36: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 08:17:36: #2 alternative fragment length(s) may be 4,129 bps INFO @ Fri, 05 Jul 2019 08:17:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.05_model.r INFO @ Fri, 05 Jul 2019 08:17:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:17:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:17:38: #2 number of paired peaks: 56584 INFO @ Fri, 05 Jul 2019 08:17:38: start model_add_line... INFO @ Fri, 05 Jul 2019 08:17:39: start X-correlation... INFO @ Fri, 05 Jul 2019 08:17:39: end of X-cor INFO @ Fri, 05 Jul 2019 08:17:39: #2 finished! INFO @ Fri, 05 Jul 2019 08:17:39: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 08:17:39: #2 alternative fragment length(s) may be 4,129 bps INFO @ Fri, 05 Jul 2019 08:17:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.10_model.r INFO @ Fri, 05 Jul 2019 08:17:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:17:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:18:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:18:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:18:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:19:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.20_peaks.xls INFO @ Fri, 05 Jul 2019 08:19:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:19:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.20_summits.bed INFO @ Fri, 05 Jul 2019 08:19:08: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (86 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:19:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.05_peaks.xls INFO @ Fri, 05 Jul 2019 08:19:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:19:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.05_summits.bed INFO @ Fri, 05 Jul 2019 08:19:12: Done! pass1 - making usageList (61 chroms): 2 millis pass2 - checking and writing primary data (4073 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:19:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.10_peaks.xls INFO @ Fri, 05 Jul 2019 08:19:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:19:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101987/ERX101987.10_summits.bed INFO @ Fri, 05 Jul 2019 08:19:13: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (776 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。