Job ID = 2002183 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,650,380 reads read : 25,650,380 reads written : 25,650,380 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: 00:00:01 Multiseed full-index search: 00:10:06 25650380 reads; of these: 25650380 (100.00%) were unpaired; of these: 824123 (3.21%) aligned 0 times 18037925 (70.32%) aligned exactly 1 time 6788332 (26.46%) aligned >1 times 96.79% overall alignment rate Time searching: 00:10:08 Overall time: 00:10:08 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] 2239876 / 24826257 = 0.0902 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 11:55:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.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 11:55:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:55:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:55:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.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 11:55:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:55:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:55:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.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 11:55:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:55:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:55:29: 1000000 INFO @ Fri, 05 Jul 2019 11:55:31: 1000000 INFO @ Fri, 05 Jul 2019 11:55:31: 1000000 INFO @ Fri, 05 Jul 2019 11:55:37: 2000000 INFO @ Fri, 05 Jul 2019 11:55:40: 2000000 INFO @ Fri, 05 Jul 2019 11:55:40: 2000000 INFO @ Fri, 05 Jul 2019 11:55:44: 3000000 INFO @ Fri, 05 Jul 2019 11:55:49: 3000000 INFO @ Fri, 05 Jul 2019 11:55:49: 3000000 INFO @ Fri, 05 Jul 2019 11:55:51: 4000000 INFO @ Fri, 05 Jul 2019 11:55:57: 4000000 INFO @ Fri, 05 Jul 2019 11:55:58: 4000000 INFO @ Fri, 05 Jul 2019 11:55:59: 5000000 INFO @ Fri, 05 Jul 2019 11:56:06: 5000000 INFO @ Fri, 05 Jul 2019 11:56:07: 6000000 INFO @ Fri, 05 Jul 2019 11:56:07: 5000000 INFO @ Fri, 05 Jul 2019 11:56:14: 7000000 INFO @ Fri, 05 Jul 2019 11:56:15: 6000000 INFO @ Fri, 05 Jul 2019 11:56:16: 6000000 INFO @ Fri, 05 Jul 2019 11:56:21: 8000000 INFO @ Fri, 05 Jul 2019 11:56:24: 7000000 INFO @ Fri, 05 Jul 2019 11:56:25: 7000000 INFO @ Fri, 05 Jul 2019 11:56:28: 9000000 INFO @ Fri, 05 Jul 2019 11:56:32: 8000000 INFO @ Fri, 05 Jul 2019 11:56:33: 8000000 INFO @ Fri, 05 Jul 2019 11:56:38: 10000000 INFO @ Fri, 05 Jul 2019 11:56:41: 9000000 INFO @ Fri, 05 Jul 2019 11:56:42: 9000000 INFO @ Fri, 05 Jul 2019 11:56:46: 11000000 INFO @ Fri, 05 Jul 2019 11:56:49: 10000000 INFO @ Fri, 05 Jul 2019 11:56:50: 10000000 INFO @ Fri, 05 Jul 2019 11:56:53: 12000000 INFO @ Fri, 05 Jul 2019 11:56:58: 11000000 INFO @ Fri, 05 Jul 2019 11:56:59: 11000000 INFO @ Fri, 05 Jul 2019 11:57:00: 13000000 INFO @ Fri, 05 Jul 2019 11:57:06: 12000000 INFO @ Fri, 05 Jul 2019 11:57:08: 12000000 INFO @ Fri, 05 Jul 2019 11:57:08: 14000000 INFO @ Fri, 05 Jul 2019 11:57:15: 13000000 INFO @ Fri, 05 Jul 2019 11:57:16: 15000000 INFO @ Fri, 05 Jul 2019 11:57:16: 13000000 INFO @ Fri, 05 Jul 2019 11:57:23: 16000000 INFO @ Fri, 05 Jul 2019 11:57:24: 14000000 INFO @ Fri, 05 Jul 2019 11:57:24: 14000000 INFO @ Fri, 05 Jul 2019 11:57:31: 17000000 INFO @ Fri, 05 Jul 2019 11:57:33: 15000000 INFO @ Fri, 05 Jul 2019 11:57:33: 15000000 INFO @ Fri, 05 Jul 2019 11:57:38: 18000000 INFO @ Fri, 05 Jul 2019 11:57:41: 16000000 INFO @ Fri, 05 Jul 2019 11:57:42: 16000000 INFO @ Fri, 05 Jul 2019 11:57:46: 19000000 INFO @ Fri, 05 Jul 2019 11:57:50: 17000000 INFO @ Fri, 05 Jul 2019 11:57:51: 17000000 INFO @ Fri, 05 Jul 2019 11:57:53: 20000000 INFO @ Fri, 05 Jul 2019 11:57:58: 18000000 INFO @ Fri, 05 Jul 2019 11:58:00: 18000000 INFO @ Fri, 05 Jul 2019 11:58:01: 21000000 INFO @ Fri, 05 Jul 2019 11:58:06: 19000000 INFO @ Fri, 05 Jul 2019 11:58:08: 22000000 INFO @ Fri, 05 Jul 2019 11:58:09: 19000000 INFO @ Fri, 05 Jul 2019 11:58:13: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:58:13: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:58:13: #1 total tags in treatment: 22586381 INFO @ Fri, 05 Jul 2019 11:58:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:58:13: #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 11:58:14: #1 tags after filtering in treatment: 22586268 INFO @ Fri, 05 Jul 2019 11:58:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:58:14: #1 finished! INFO @ Fri, 05 Jul 2019 11:58:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:58:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:58:14: 20000000 INFO @ Fri, 05 Jul 2019 11:58:17: 20000000 INFO @ Fri, 05 Jul 2019 11:58:17: #2 number of paired peaks: 31673 INFO @ Fri, 05 Jul 2019 11:58:17: start model_add_line... INFO @ Fri, 05 Jul 2019 11:58:18: start X-correlation... INFO @ Fri, 05 Jul 2019 11:58:18: end of X-cor INFO @ Fri, 05 Jul 2019 11:58:18: #2 finished! INFO @ Fri, 05 Jul 2019 11:58:18: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 11:58:18: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 11:58:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.05_model.r INFO @ Fri, 05 Jul 2019 11:58:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:58:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:58:23: 21000000 INFO @ Fri, 05 Jul 2019 11:58:26: 21000000 INFO @ Fri, 05 Jul 2019 11:58:31: 22000000 INFO @ Fri, 05 Jul 2019 11:58:34: 22000000 INFO @ Fri, 05 Jul 2019 11:58:36: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:58:36: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:58:36: #1 total tags in treatment: 22586381 INFO @ Fri, 05 Jul 2019 11:58:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:58:36: #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 11:58:36: #1 tags after filtering in treatment: 22586268 INFO @ Fri, 05 Jul 2019 11:58:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:58:36: #1 finished! INFO @ Fri, 05 Jul 2019 11:58:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:58:39: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:58:39: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:58:39: #1 total tags in treatment: 22586381 INFO @ Fri, 05 Jul 2019 11:58:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:58:39: #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 11:58:40: #1 tags after filtering in treatment: 22586268 INFO @ Fri, 05 Jul 2019 11:58:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:58:40: #1 finished! INFO @ Fri, 05 Jul 2019 11:58:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:58:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:58:40: #2 number of paired peaks: 31673 INFO @ Fri, 05 Jul 2019 11:58:40: start model_add_line... INFO @ Fri, 05 Jul 2019 11:58:40: start X-correlation... INFO @ Fri, 05 Jul 2019 11:58:40: end of X-cor INFO @ Fri, 05 Jul 2019 11:58:40: #2 finished! INFO @ Fri, 05 Jul 2019 11:58:40: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 11:58:40: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 11:58:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.20_model.r INFO @ Fri, 05 Jul 2019 11:58:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:58:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:58:44: #2 number of paired peaks: 31673 INFO @ Fri, 05 Jul 2019 11:58:44: start model_add_line... INFO @ Fri, 05 Jul 2019 11:58:44: start X-correlation... INFO @ Fri, 05 Jul 2019 11:58:44: end of X-cor INFO @ Fri, 05 Jul 2019 11:58:44: #2 finished! INFO @ Fri, 05 Jul 2019 11:58:44: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 11:58:44: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 11:58:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.10_model.r INFO @ Fri, 05 Jul 2019 11:58:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:59:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:59:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:59:55: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:00:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.05_summits.bed INFO @ Fri, 05 Jul 2019 12:00:08: Done! pass1 - making usageList (94 chroms): 10 millis pass2 - checking and writing primary data (26060 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:00:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:00:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:00:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.20_summits.bed INFO @ Fri, 05 Jul 2019 12:00:29: Done! pass1 - making usageList (47 chroms): 5 millis pass2 - checking and writing primary data (8988 records, 4 fields): 19 millis INFO @ Fri, 05 Jul 2019 12:00:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:00:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:00:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210292/ERX210292.10_summits.bed INFO @ Fri, 05 Jul 2019 12:00:32: Done! pass1 - making usageList (76 chroms): 7 millis pass2 - checking and writing primary data (16715 records, 4 fields): 28 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。