Job ID = 2002155 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,827,558 reads read : 30,827,558 reads written : 30,827,558 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:11:50 30827558 reads; of these: 30827558 (100.00%) were unpaired; of these: 846926 (2.75%) aligned 0 times 21608568 (70.09%) aligned exactly 1 time 8372064 (27.16%) aligned >1 times 97.25% overall alignment rate Time searching: 00:11:53 Overall time: 00:11:53 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] 1116144 / 29980632 = 0.0372 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 11:09:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.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 11:09:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:09:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:09:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.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 11:09:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:09:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.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 11:09:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:09:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:09:55: 1000000 INFO @ Fri, 05 Jul 2019 11:09:56: 1000000 INFO @ Fri, 05 Jul 2019 11:09:57: 1000000 INFO @ Fri, 05 Jul 2019 11:10:03: 2000000 INFO @ Fri, 05 Jul 2019 11:10:04: 2000000 INFO @ Fri, 05 Jul 2019 11:10:05: 2000000 INFO @ Fri, 05 Jul 2019 11:10:10: 3000000 INFO @ Fri, 05 Jul 2019 11:10:12: 3000000 INFO @ Fri, 05 Jul 2019 11:10:13: 3000000 INFO @ Fri, 05 Jul 2019 11:10:17: 4000000 INFO @ Fri, 05 Jul 2019 11:10:21: 4000000 INFO @ Fri, 05 Jul 2019 11:10:22: 4000000 INFO @ Fri, 05 Jul 2019 11:10:26: 5000000 INFO @ Fri, 05 Jul 2019 11:10:29: 5000000 INFO @ Fri, 05 Jul 2019 11:10:30: 5000000 INFO @ Fri, 05 Jul 2019 11:10:33: 6000000 INFO @ Fri, 05 Jul 2019 11:10:38: 6000000 INFO @ Fri, 05 Jul 2019 11:10:38: 6000000 INFO @ Fri, 05 Jul 2019 11:10:40: 7000000 INFO @ Fri, 05 Jul 2019 11:10:46: 7000000 INFO @ Fri, 05 Jul 2019 11:10:47: 7000000 INFO @ Fri, 05 Jul 2019 11:10:47: 8000000 INFO @ Fri, 05 Jul 2019 11:10:54: 8000000 INFO @ Fri, 05 Jul 2019 11:10:54: 9000000 INFO @ Fri, 05 Jul 2019 11:10:55: 8000000 INFO @ Fri, 05 Jul 2019 11:11:01: 10000000 INFO @ Fri, 05 Jul 2019 11:11:02: 9000000 INFO @ Fri, 05 Jul 2019 11:11:03: 9000000 INFO @ Fri, 05 Jul 2019 11:11:09: 11000000 INFO @ Fri, 05 Jul 2019 11:11:10: 10000000 INFO @ Fri, 05 Jul 2019 11:11:11: 10000000 INFO @ Fri, 05 Jul 2019 11:11:15: 12000000 INFO @ Fri, 05 Jul 2019 11:11:18: 11000000 INFO @ Fri, 05 Jul 2019 11:11:18: 11000000 INFO @ Fri, 05 Jul 2019 11:11:23: 13000000 INFO @ Fri, 05 Jul 2019 11:11:26: 12000000 INFO @ Fri, 05 Jul 2019 11:11:26: 12000000 INFO @ Fri, 05 Jul 2019 11:11:30: 14000000 INFO @ Fri, 05 Jul 2019 11:11:34: 13000000 INFO @ Fri, 05 Jul 2019 11:11:34: 13000000 INFO @ Fri, 05 Jul 2019 11:11:37: 15000000 INFO @ Fri, 05 Jul 2019 11:11:42: 14000000 INFO @ Fri, 05 Jul 2019 11:11:42: 14000000 INFO @ Fri, 05 Jul 2019 11:11:44: 16000000 INFO @ Fri, 05 Jul 2019 11:11:49: 15000000 INFO @ Fri, 05 Jul 2019 11:11:50: 15000000 INFO @ Fri, 05 Jul 2019 11:11:51: 17000000 INFO @ Fri, 05 Jul 2019 11:11:57: 16000000 INFO @ Fri, 05 Jul 2019 11:11:57: 16000000 INFO @ Fri, 05 Jul 2019 11:11:58: 18000000 INFO @ Fri, 05 Jul 2019 11:12:05: 17000000 INFO @ Fri, 05 Jul 2019 11:12:05: 17000000 INFO @ Fri, 05 Jul 2019 11:12:05: 19000000 INFO @ Fri, 05 Jul 2019 11:12:12: 20000000 INFO @ Fri, 05 Jul 2019 11:12:12: 18000000 INFO @ Fri, 05 Jul 2019 11:12:13: 18000000 INFO @ Fri, 05 Jul 2019 11:12:19: 21000000 INFO @ Fri, 05 Jul 2019 11:12:20: 19000000 INFO @ Fri, 05 Jul 2019 11:12:20: 19000000 INFO @ Fri, 05 Jul 2019 11:12:26: 22000000 INFO @ Fri, 05 Jul 2019 11:12:28: 20000000 INFO @ Fri, 05 Jul 2019 11:12:28: 20000000 INFO @ Fri, 05 Jul 2019 11:12:34: 23000000 INFO @ Fri, 05 Jul 2019 11:12:36: 21000000 INFO @ Fri, 05 Jul 2019 11:12:36: 21000000 INFO @ Fri, 05 Jul 2019 11:12:41: 24000000 INFO @ Fri, 05 Jul 2019 11:12:43: 22000000 INFO @ Fri, 05 Jul 2019 11:12:44: 22000000 INFO @ Fri, 05 Jul 2019 11:12:48: 25000000 INFO @ Fri, 05 Jul 2019 11:12:52: 23000000 INFO @ Fri, 05 Jul 2019 11:12:52: 23000000 INFO @ Fri, 05 Jul 2019 11:12:56: 26000000 INFO @ Fri, 05 Jul 2019 11:13:01: 24000000 INFO @ Fri, 05 Jul 2019 11:13:01: 24000000 INFO @ Fri, 05 Jul 2019 11:13:03: 27000000 INFO @ Fri, 05 Jul 2019 11:13:10: 25000000 INFO @ Fri, 05 Jul 2019 11:13:10: 25000000 INFO @ Fri, 05 Jul 2019 11:13:11: 28000000 INFO @ Fri, 05 Jul 2019 11:13:17: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:13:17: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:13:17: #1 total tags in treatment: 28864488 INFO @ Fri, 05 Jul 2019 11:13:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:13:17: #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 11:13:18: #1 tags after filtering in treatment: 28864368 INFO @ Fri, 05 Jul 2019 11:13:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:13:18: #1 finished! INFO @ Fri, 05 Jul 2019 11:13:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:13:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:13:18: 26000000 INFO @ Fri, 05 Jul 2019 11:13:18: 26000000 INFO @ Fri, 05 Jul 2019 11:13:22: #2 number of paired peaks: 20092 INFO @ Fri, 05 Jul 2019 11:13:22: start model_add_line... INFO @ Fri, 05 Jul 2019 11:13:22: start X-correlation... INFO @ Fri, 05 Jul 2019 11:13:22: end of X-cor INFO @ Fri, 05 Jul 2019 11:13:22: #2 finished! INFO @ Fri, 05 Jul 2019 11:13:22: #2 predicted fragment length is 125 bps INFO @ Fri, 05 Jul 2019 11:13:22: #2 alternative fragment length(s) may be 4,125,284 bps INFO @ Fri, 05 Jul 2019 11:13:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.05_model.r INFO @ Fri, 05 Jul 2019 11:13:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:13:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:13:27: 27000000 INFO @ Fri, 05 Jul 2019 11:13:27: 27000000 INFO @ Fri, 05 Jul 2019 11:13:36: 28000000 INFO @ Fri, 05 Jul 2019 11:13:36: 28000000 INFO @ Fri, 05 Jul 2019 11:13:43: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:13:43: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:13:43: #1 total tags in treatment: 28864488 INFO @ Fri, 05 Jul 2019 11:13:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:13:43: #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 11:13:43: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:13:43: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:13:43: #1 total tags in treatment: 28864488 INFO @ Fri, 05 Jul 2019 11:13:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:13:43: #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 11:13:44: #1 tags after filtering in treatment: 28864368 INFO @ Fri, 05 Jul 2019 11:13:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:13:44: #1 finished! INFO @ Fri, 05 Jul 2019 11:13:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:13:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:13:44: #1 tags after filtering in treatment: 28864368 INFO @ Fri, 05 Jul 2019 11:13:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:13:44: #1 finished! INFO @ Fri, 05 Jul 2019 11:13:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:13:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:13:48: #2 number of paired peaks: 20092 INFO @ Fri, 05 Jul 2019 11:13:48: start model_add_line... INFO @ Fri, 05 Jul 2019 11:13:48: start X-correlation... INFO @ Fri, 05 Jul 2019 11:13:48: end of X-cor INFO @ Fri, 05 Jul 2019 11:13:48: #2 finished! INFO @ Fri, 05 Jul 2019 11:13:48: #2 predicted fragment length is 125 bps INFO @ Fri, 05 Jul 2019 11:13:48: #2 alternative fragment length(s) may be 4,125,284 bps INFO @ Fri, 05 Jul 2019 11:13:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.20_model.r INFO @ Fri, 05 Jul 2019 11:13:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:13:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:13:48: #2 number of paired peaks: 20092 INFO @ Fri, 05 Jul 2019 11:13:48: start model_add_line... INFO @ Fri, 05 Jul 2019 11:13:49: start X-correlation... INFO @ Fri, 05 Jul 2019 11:13:49: end of X-cor INFO @ Fri, 05 Jul 2019 11:13:49: #2 finished! INFO @ Fri, 05 Jul 2019 11:13:49: #2 predicted fragment length is 125 bps INFO @ Fri, 05 Jul 2019 11:13:49: #2 alternative fragment length(s) may be 4,125,284 bps INFO @ Fri, 05 Jul 2019 11:13:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.10_model.r INFO @ Fri, 05 Jul 2019 11:13:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:13:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:14:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:15:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:15:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:15:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:15:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:15:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.05_summits.bed INFO @ Fri, 05 Jul 2019 11:15:44: Done! pass1 - making usageList (48 chroms): 3 millis pass2 - checking and writing primary data (1537 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:16:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:16:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:16:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.20_summits.bed INFO @ Fri, 05 Jul 2019 11:16:09: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 83 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:16:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:16:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:16:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102048/ERX102048.10_summits.bed INFO @ Fri, 05 Jul 2019 11:16:14: Done! pass1 - making usageList (36 chroms): 2 millis pass2 - checking and writing primary data (386 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。