Job ID = 2001140 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,888,887 reads read : 23,888,887 reads written : 23,888,887 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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:06:40 23888887 reads; of these: 23888887 (100.00%) were unpaired; of these: 675380 (2.83%) aligned 0 times 18833545 (78.84%) aligned exactly 1 time 4379962 (18.33%) aligned >1 times 97.17% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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] 4322991 / 23213507 = 0.1862 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 03:43:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.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 03:43:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:43:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:43:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.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 03:43:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:43:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:43:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.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 03:43:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:43:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:43:51: 1000000 INFO @ Fri, 05 Jul 2019 03:43:52: 1000000 INFO @ Fri, 05 Jul 2019 03:43:53: 1000000 INFO @ Fri, 05 Jul 2019 03:43:57: 2000000 INFO @ Fri, 05 Jul 2019 03:43:58: 2000000 INFO @ Fri, 05 Jul 2019 03:43:59: 2000000 INFO @ Fri, 05 Jul 2019 03:44:02: 3000000 INFO @ Fri, 05 Jul 2019 03:44:04: 3000000 INFO @ Fri, 05 Jul 2019 03:44:05: 3000000 INFO @ Fri, 05 Jul 2019 03:44:08: 4000000 INFO @ Fri, 05 Jul 2019 03:44:09: 4000000 INFO @ Fri, 05 Jul 2019 03:44:10: 4000000 INFO @ Fri, 05 Jul 2019 03:44:13: 5000000 INFO @ Fri, 05 Jul 2019 03:44:15: 5000000 INFO @ Fri, 05 Jul 2019 03:44:16: 5000000 INFO @ Fri, 05 Jul 2019 03:44:18: 6000000 INFO @ Fri, 05 Jul 2019 03:44:21: 6000000 INFO @ Fri, 05 Jul 2019 03:44:22: 6000000 INFO @ Fri, 05 Jul 2019 03:44:24: 7000000 INFO @ Fri, 05 Jul 2019 03:44:26: 7000000 INFO @ Fri, 05 Jul 2019 03:44:28: 7000000 INFO @ Fri, 05 Jul 2019 03:44:29: 8000000 INFO @ Fri, 05 Jul 2019 03:44:32: 8000000 INFO @ Fri, 05 Jul 2019 03:44:33: 8000000 INFO @ Fri, 05 Jul 2019 03:44:34: 9000000 INFO @ Fri, 05 Jul 2019 03:44:38: 9000000 INFO @ Fri, 05 Jul 2019 03:44:39: 9000000 INFO @ Fri, 05 Jul 2019 03:44:40: 10000000 INFO @ Fri, 05 Jul 2019 03:44:44: 10000000 INFO @ Fri, 05 Jul 2019 03:44:45: 10000000 INFO @ Fri, 05 Jul 2019 03:44:45: 11000000 INFO @ Fri, 05 Jul 2019 03:44:49: 11000000 INFO @ Fri, 05 Jul 2019 03:44:50: 12000000 INFO @ Fri, 05 Jul 2019 03:44:51: 11000000 INFO @ Fri, 05 Jul 2019 03:44:55: 12000000 INFO @ Fri, 05 Jul 2019 03:44:56: 13000000 INFO @ Fri, 05 Jul 2019 03:44:56: 12000000 INFO @ Fri, 05 Jul 2019 03:45:01: 13000000 INFO @ Fri, 05 Jul 2019 03:45:01: 14000000 INFO @ Fri, 05 Jul 2019 03:45:02: 13000000 INFO @ Fri, 05 Jul 2019 03:45:07: 15000000 INFO @ Fri, 05 Jul 2019 03:45:07: 14000000 INFO @ Fri, 05 Jul 2019 03:45:08: 14000000 INFO @ Fri, 05 Jul 2019 03:45:12: 16000000 INFO @ Fri, 05 Jul 2019 03:45:12: 15000000 INFO @ Fri, 05 Jul 2019 03:45:13: 15000000 INFO @ Fri, 05 Jul 2019 03:45:17: 17000000 INFO @ Fri, 05 Jul 2019 03:45:18: 16000000 INFO @ Fri, 05 Jul 2019 03:45:19: 16000000 INFO @ Fri, 05 Jul 2019 03:45:23: 18000000 INFO @ Fri, 05 Jul 2019 03:45:24: 17000000 INFO @ Fri, 05 Jul 2019 03:45:25: 17000000 INFO @ Fri, 05 Jul 2019 03:45:28: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:45:28: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:45:28: #1 total tags in treatment: 18890516 INFO @ Fri, 05 Jul 2019 03:45:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:45:28: #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 03:45:28: #1 tags after filtering in treatment: 18890306 INFO @ Fri, 05 Jul 2019 03:45:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:45:28: #1 finished! INFO @ Fri, 05 Jul 2019 03:45:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:45:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:45:29: 18000000 INFO @ Fri, 05 Jul 2019 03:45:30: 18000000 INFO @ Fri, 05 Jul 2019 03:45:31: #2 number of paired peaks: 29477 INFO @ Fri, 05 Jul 2019 03:45:31: start model_add_line... INFO @ Fri, 05 Jul 2019 03:45:31: start X-correlation... INFO @ Fri, 05 Jul 2019 03:45:31: end of X-cor INFO @ Fri, 05 Jul 2019 03:45:31: #2 finished! INFO @ Fri, 05 Jul 2019 03:45:31: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 03:45:31: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 05 Jul 2019 03:45:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.05_model.r INFO @ Fri, 05 Jul 2019 03:45:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:45:35: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:45:35: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:45:35: #1 total tags in treatment: 18890516 INFO @ Fri, 05 Jul 2019 03:45:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:45:35: #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 03:45:35: #1 tags after filtering in treatment: 18890306 INFO @ Fri, 05 Jul 2019 03:45:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:45:35: #1 finished! INFO @ Fri, 05 Jul 2019 03:45:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:45:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:45:36: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:45:36: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:45:36: #1 total tags in treatment: 18890516 INFO @ Fri, 05 Jul 2019 03:45:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:45:36: #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 03:45:36: #1 tags after filtering in treatment: 18890306 INFO @ Fri, 05 Jul 2019 03:45:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:45:36: #1 finished! INFO @ Fri, 05 Jul 2019 03:45:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:45:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:45:38: #2 number of paired peaks: 29477 INFO @ Fri, 05 Jul 2019 03:45:38: start model_add_line... INFO @ Fri, 05 Jul 2019 03:45:38: start X-correlation... INFO @ Fri, 05 Jul 2019 03:45:38: end of X-cor INFO @ Fri, 05 Jul 2019 03:45:38: #2 finished! INFO @ Fri, 05 Jul 2019 03:45:38: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 03:45:38: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 05 Jul 2019 03:45:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.10_model.r INFO @ Fri, 05 Jul 2019 03:45:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:45:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:45:39: #2 number of paired peaks: 29477 INFO @ Fri, 05 Jul 2019 03:45:39: start model_add_line... INFO @ Fri, 05 Jul 2019 03:45:39: start X-correlation... INFO @ Fri, 05 Jul 2019 03:45:39: end of X-cor INFO @ Fri, 05 Jul 2019 03:45:39: #2 finished! INFO @ Fri, 05 Jul 2019 03:45:39: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 03:45:39: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 05 Jul 2019 03:45:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.20_model.r INFO @ Fri, 05 Jul 2019 03:45:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:45:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:46:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:46:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:46:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:46:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.05_peaks.xls INFO @ Fri, 05 Jul 2019 03:46:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:46:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.05_summits.bed INFO @ Fri, 05 Jul 2019 03:46:36: Done! pass1 - making usageList (120 chroms): 5 millis pass2 - checking and writing primary data (28523 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 03:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.10_peaks.xls INFO @ Fri, 05 Jul 2019 03:46:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:46:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.10_summits.bed INFO @ Fri, 05 Jul 2019 03:46:43: Done! INFO @ Fri, 05 Jul 2019 03:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.20_peaks.xls INFO @ Fri, 05 Jul 2019 03:46:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:46:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX032774/ERX032774.20_summits.bed INFO @ Fri, 05 Jul 2019 03:46:44: Done! pass1 - making usageList (97 chroms): 4 millis pass2 - checking and writing primary data (23838 records, 4 fields): 33 millis CompletedMACS2peakCalling pass1 - making usageList (76 chroms): 3 millis pass2 - checking and writing primary data (19026 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。