Job ID = 2001718 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,218,555 reads read : 27,218,555 reads written : 27,218,555 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: 00:05:42 27218555 reads; of these: 27218555 (100.00%) were unpaired; of these: 523383 (1.92%) aligned 0 times 23792102 (87.41%) aligned exactly 1 time 2903070 (10.67%) aligned >1 times 98.08% overall alignment rate Time searching: 00:05:45 Overall time: 00:05:45 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] 12300180 / 26695172 = 0.4608 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 09:53:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.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 09:53:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:53:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:53:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.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 09:53:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:53:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:53:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.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 09:53:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:53:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:53:50: 1000000 INFO @ Fri, 05 Jul 2019 09:53:50: 1000000 INFO @ Fri, 05 Jul 2019 09:53:51: 1000000 INFO @ Fri, 05 Jul 2019 09:53:58: 2000000 INFO @ Fri, 05 Jul 2019 09:53:59: 2000000 INFO @ Fri, 05 Jul 2019 09:54:00: 2000000 INFO @ Fri, 05 Jul 2019 09:54:07: 3000000 INFO @ Fri, 05 Jul 2019 09:54:07: 3000000 INFO @ Fri, 05 Jul 2019 09:54:09: 3000000 INFO @ Fri, 05 Jul 2019 09:54:15: 4000000 INFO @ Fri, 05 Jul 2019 09:54:16: 4000000 INFO @ Fri, 05 Jul 2019 09:54:17: 4000000 INFO @ Fri, 05 Jul 2019 09:54:23: 5000000 INFO @ Fri, 05 Jul 2019 09:54:24: 5000000 INFO @ Fri, 05 Jul 2019 09:54:26: 5000000 INFO @ Fri, 05 Jul 2019 09:54:31: 6000000 INFO @ Fri, 05 Jul 2019 09:54:33: 6000000 INFO @ Fri, 05 Jul 2019 09:54:34: 6000000 INFO @ Fri, 05 Jul 2019 09:54:39: 7000000 INFO @ Fri, 05 Jul 2019 09:54:41: 7000000 INFO @ Fri, 05 Jul 2019 09:54:43: 7000000 INFO @ Fri, 05 Jul 2019 09:54:47: 8000000 INFO @ Fri, 05 Jul 2019 09:54:50: 8000000 INFO @ Fri, 05 Jul 2019 09:54:52: 8000000 INFO @ Fri, 05 Jul 2019 09:54:56: 9000000 INFO @ Fri, 05 Jul 2019 09:54:59: 9000000 INFO @ Fri, 05 Jul 2019 09:55:01: 9000000 INFO @ Fri, 05 Jul 2019 09:55:04: 10000000 INFO @ Fri, 05 Jul 2019 09:55:07: 10000000 INFO @ Fri, 05 Jul 2019 09:55:09: 10000000 INFO @ Fri, 05 Jul 2019 09:55:12: 11000000 INFO @ Fri, 05 Jul 2019 09:55:16: 11000000 INFO @ Fri, 05 Jul 2019 09:55:18: 11000000 INFO @ Fri, 05 Jul 2019 09:55:20: 12000000 INFO @ Fri, 05 Jul 2019 09:55:25: 12000000 INFO @ Fri, 05 Jul 2019 09:55:27: 12000000 INFO @ Fri, 05 Jul 2019 09:55:28: 13000000 INFO @ Fri, 05 Jul 2019 09:55:33: 13000000 INFO @ Fri, 05 Jul 2019 09:55:36: 13000000 INFO @ Fri, 05 Jul 2019 09:55:37: 14000000 INFO @ Fri, 05 Jul 2019 09:55:40: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:55:40: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:55:40: #1 total tags in treatment: 14394992 INFO @ Fri, 05 Jul 2019 09:55:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:55:40: #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 09:55:40: #1 tags after filtering in treatment: 14394715 INFO @ Fri, 05 Jul 2019 09:55:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:55:40: #1 finished! INFO @ Fri, 05 Jul 2019 09:55:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:55:42: 14000000 INFO @ Fri, 05 Jul 2019 09:55:44: #2 number of paired peaks: 52068 INFO @ Fri, 05 Jul 2019 09:55:44: start model_add_line... INFO @ Fri, 05 Jul 2019 09:55:44: 14000000 INFO @ Fri, 05 Jul 2019 09:55:44: start X-correlation... INFO @ Fri, 05 Jul 2019 09:55:44: end of X-cor INFO @ Fri, 05 Jul 2019 09:55:44: #2 finished! INFO @ Fri, 05 Jul 2019 09:55:44: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 09:55:44: #2 alternative fragment length(s) may be 4,137 bps INFO @ Fri, 05 Jul 2019 09:55:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.10_model.r INFO @ Fri, 05 Jul 2019 09:55:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:55:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:55:45: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:55:45: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:55:45: #1 total tags in treatment: 14394992 INFO @ Fri, 05 Jul 2019 09:55:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:55:45: #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 09:55:46: #1 tags after filtering in treatment: 14394715 INFO @ Fri, 05 Jul 2019 09:55:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:55:46: #1 finished! INFO @ Fri, 05 Jul 2019 09:55:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:55:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:55:48: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:55:48: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:55:48: #1 total tags in treatment: 14394992 INFO @ Fri, 05 Jul 2019 09:55:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:55:48: #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 09:55:48: #1 tags after filtering in treatment: 14394715 INFO @ Fri, 05 Jul 2019 09:55:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:55:48: #1 finished! INFO @ Fri, 05 Jul 2019 09:55:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:55:50: #2 number of paired peaks: 52068 INFO @ Fri, 05 Jul 2019 09:55:50: start model_add_line... INFO @ Fri, 05 Jul 2019 09:55:50: start X-correlation... INFO @ Fri, 05 Jul 2019 09:55:50: end of X-cor INFO @ Fri, 05 Jul 2019 09:55:50: #2 finished! INFO @ Fri, 05 Jul 2019 09:55:50: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 09:55:50: #2 alternative fragment length(s) may be 4,137 bps INFO @ Fri, 05 Jul 2019 09:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.05_model.r INFO @ Fri, 05 Jul 2019 09:55:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:55:52: #2 number of paired peaks: 52068 INFO @ Fri, 05 Jul 2019 09:55:52: start model_add_line... INFO @ Fri, 05 Jul 2019 09:55:52: start X-correlation... INFO @ Fri, 05 Jul 2019 09:55:52: end of X-cor INFO @ Fri, 05 Jul 2019 09:55:52: #2 finished! INFO @ Fri, 05 Jul 2019 09:55:52: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 09:55:52: #2 alternative fragment length(s) may be 4,137 bps INFO @ Fri, 05 Jul 2019 09:55:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.20_model.r INFO @ Fri, 05 Jul 2019 09:55:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:55:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:56:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:56:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:56:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:56:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:56:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:56:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.10_summits.bed INFO @ Fri, 05 Jul 2019 09:56:53: Done! pass1 - making usageList (114 chroms): 12 millis pass2 - checking and writing primary data (34640 records, 4 fields): 55 millis INFO @ Fri, 05 Jul 2019 09:56:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:56:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:56:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.05_summits.bed INFO @ Fri, 05 Jul 2019 09:56:58: Done! pass1 - making usageList (139 chroms): 14 millis pass2 - checking and writing primary data (44970 records, 4 fields): 61 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:57:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102022/ERX102022.20_summits.bed CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:57:01: Done! pass1 - making usageList (86 chroms): 6 millis pass2 - checking and writing primary data (22778 records, 4 fields): 33 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。