Job ID = 2001694 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,119,826 reads read : 22,119,826 reads written : 22,119,826 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:01 22119826 reads; of these: 22119826 (100.00%) were unpaired; of these: 473546 (2.14%) aligned 0 times 16326014 (73.81%) aligned exactly 1 time 5320266 (24.05%) aligned >1 times 97.86% overall alignment rate Time searching: 00:09:04 Overall time: 00:09:04 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] 1235380 / 21646280 = 0.0571 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 09:02:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.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 09:02:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:02:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:02:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.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 09:02:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:02:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:02:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.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 09:02:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:02:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:02:37: 1000000 INFO @ Fri, 05 Jul 2019 09:02:38: 1000000 INFO @ Fri, 05 Jul 2019 09:02:40: 1000000 INFO @ Fri, 05 Jul 2019 09:02:46: 2000000 INFO @ Fri, 05 Jul 2019 09:02:46: 2000000 INFO @ Fri, 05 Jul 2019 09:02:49: 2000000 INFO @ Fri, 05 Jul 2019 09:02:55: 3000000 INFO @ Fri, 05 Jul 2019 09:02:55: 3000000 INFO @ Fri, 05 Jul 2019 09:02:57: 3000000 INFO @ Fri, 05 Jul 2019 09:03:03: 4000000 INFO @ Fri, 05 Jul 2019 09:03:04: 4000000 INFO @ Fri, 05 Jul 2019 09:03:07: 4000000 INFO @ Fri, 05 Jul 2019 09:03:12: 5000000 INFO @ Fri, 05 Jul 2019 09:03:13: 5000000 INFO @ Fri, 05 Jul 2019 09:03:15: 5000000 INFO @ Fri, 05 Jul 2019 09:03:20: 6000000 INFO @ Fri, 05 Jul 2019 09:03:21: 6000000 INFO @ Fri, 05 Jul 2019 09:03:24: 6000000 INFO @ Fri, 05 Jul 2019 09:03:29: 7000000 INFO @ Fri, 05 Jul 2019 09:03:30: 7000000 INFO @ Fri, 05 Jul 2019 09:03:33: 7000000 INFO @ Fri, 05 Jul 2019 09:03:36: 8000000 INFO @ Fri, 05 Jul 2019 09:03:39: 8000000 INFO @ Fri, 05 Jul 2019 09:03:43: 8000000 INFO @ Fri, 05 Jul 2019 09:03:44: 9000000 INFO @ Fri, 05 Jul 2019 09:03:48: 9000000 INFO @ Fri, 05 Jul 2019 09:03:51: 10000000 INFO @ Fri, 05 Jul 2019 09:03:52: 9000000 INFO @ Fri, 05 Jul 2019 09:03:57: 10000000 INFO @ Fri, 05 Jul 2019 09:03:58: 11000000 INFO @ Fri, 05 Jul 2019 09:04:01: 10000000 INFO @ Fri, 05 Jul 2019 09:04:07: 11000000 INFO @ Fri, 05 Jul 2019 09:04:09: 12000000 INFO @ Fri, 05 Jul 2019 09:04:10: 11000000 INFO @ Fri, 05 Jul 2019 09:04:17: 12000000 INFO @ Fri, 05 Jul 2019 09:04:19: 12000000 INFO @ Fri, 05 Jul 2019 09:04:20: 13000000 INFO @ Fri, 05 Jul 2019 09:04:27: 13000000 INFO @ Fri, 05 Jul 2019 09:04:28: 13000000 INFO @ Fri, 05 Jul 2019 09:04:29: 14000000 INFO @ Fri, 05 Jul 2019 09:04:37: 14000000 INFO @ Fri, 05 Jul 2019 09:04:37: 14000000 INFO @ Fri, 05 Jul 2019 09:04:39: 15000000 INFO @ Fri, 05 Jul 2019 09:04:46: 15000000 INFO @ Fri, 05 Jul 2019 09:04:46: 15000000 INFO @ Fri, 05 Jul 2019 09:04:48: 16000000 INFO @ Fri, 05 Jul 2019 09:04:54: 16000000 INFO @ Fri, 05 Jul 2019 09:04:55: 16000000 INFO @ Fri, 05 Jul 2019 09:04:57: 17000000 INFO @ Fri, 05 Jul 2019 09:05:03: 17000000 INFO @ Fri, 05 Jul 2019 09:05:04: 17000000 INFO @ Fri, 05 Jul 2019 09:05:06: 18000000 INFO @ Fri, 05 Jul 2019 09:05:12: 18000000 INFO @ Fri, 05 Jul 2019 09:05:13: 18000000 INFO @ Fri, 05 Jul 2019 09:05:16: 19000000 INFO @ Fri, 05 Jul 2019 09:05:21: 19000000 INFO @ Fri, 05 Jul 2019 09:05:22: 19000000 INFO @ Fri, 05 Jul 2019 09:05:26: 20000000 INFO @ Fri, 05 Jul 2019 09:05:30: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:05:30: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:05:30: #1 total tags in treatment: 20410900 INFO @ Fri, 05 Jul 2019 09:05:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:05:30: #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 09:05:30: 20000000 INFO @ Fri, 05 Jul 2019 09:05:31: #1 tags after filtering in treatment: 20410738 INFO @ Fri, 05 Jul 2019 09:05:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:05:31: #1 finished! INFO @ Fri, 05 Jul 2019 09:05:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:05:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:05:32: 20000000 INFO @ Fri, 05 Jul 2019 09:05:34: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:05:34: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:05:34: #1 total tags in treatment: 20410900 INFO @ Fri, 05 Jul 2019 09:05:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:05:34: #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 09:05:35: #1 tags after filtering in treatment: 20410738 INFO @ Fri, 05 Jul 2019 09:05:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:05:35: #1 finished! INFO @ Fri, 05 Jul 2019 09:05:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:05:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:05:35: #2 number of paired peaks: 60159 INFO @ Fri, 05 Jul 2019 09:05:35: start model_add_line... INFO @ Fri, 05 Jul 2019 09:05:36: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:05:36: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:05:36: #1 total tags in treatment: 20410900 INFO @ Fri, 05 Jul 2019 09:05:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:05:36: #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 09:05:36: start X-correlation... INFO @ Fri, 05 Jul 2019 09:05:36: end of X-cor INFO @ Fri, 05 Jul 2019 09:05:36: #2 finished! INFO @ Fri, 05 Jul 2019 09:05:36: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 09:05:36: #2 alternative fragment length(s) may be 4,131,491 bps INFO @ Fri, 05 Jul 2019 09:05:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.05_model.r INFO @ Fri, 05 Jul 2019 09:05:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:05:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:05:36: #1 tags after filtering in treatment: 20410738 INFO @ Fri, 05 Jul 2019 09:05:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:05:36: #1 finished! INFO @ Fri, 05 Jul 2019 09:05:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:05:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:05:39: #2 number of paired peaks: 60159 INFO @ Fri, 05 Jul 2019 09:05:39: start model_add_line... INFO @ Fri, 05 Jul 2019 09:05:40: start X-correlation... INFO @ Fri, 05 Jul 2019 09:05:40: end of X-cor INFO @ Fri, 05 Jul 2019 09:05:40: #2 finished! INFO @ Fri, 05 Jul 2019 09:05:40: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 09:05:40: #2 alternative fragment length(s) may be 4,131,491 bps INFO @ Fri, 05 Jul 2019 09:05:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.10_model.r INFO @ Fri, 05 Jul 2019 09:05:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:05:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:05:41: #2 number of paired peaks: 60159 INFO @ Fri, 05 Jul 2019 09:05:41: start model_add_line... INFO @ Fri, 05 Jul 2019 09:05:41: start X-correlation... INFO @ Fri, 05 Jul 2019 09:05:41: end of X-cor INFO @ Fri, 05 Jul 2019 09:05:41: #2 finished! INFO @ Fri, 05 Jul 2019 09:05:41: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 09:05:41: #2 alternative fragment length(s) may be 4,131,491 bps INFO @ Fri, 05 Jul 2019 09:05:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.20_model.r INFO @ Fri, 05 Jul 2019 09:05:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:05:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:06:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:06:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:06:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:07:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:07:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:07:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.05_summits.bed INFO @ Fri, 05 Jul 2019 09:07:18: Done! pass1 - making usageList (57 chroms): 2 millis pass2 - checking and writing primary data (3376 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:07:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:07:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.10_summits.bed INFO @ Fri, 05 Jul 2019 09:07:22: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (651 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:07:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:07:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:07:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102004/ERX102004.20_summits.bed INFO @ Fri, 05 Jul 2019 09:07:24: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (89 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。