Job ID = 2001147 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,625,313 reads read : 21,625,313 reads written : 21,625,313 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:28 21625313 reads; of these: 21625313 (100.00%) were unpaired; of these: 526568 (2.43%) aligned 0 times 15829952 (73.20%) aligned exactly 1 time 5268793 (24.36%) aligned >1 times 97.57% overall alignment rate Time searching: 00:09:32 Overall time: 00:09:32 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] 1078325 / 21098745 = 0.0511 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 04:01:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.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 04:01:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:01:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:01:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.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 04:01:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:01:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:01:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.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 04:01:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:01:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:01:26: 1000000 INFO @ Fri, 05 Jul 2019 04:01:28: 1000000 INFO @ Fri, 05 Jul 2019 04:01:29: 1000000 INFO @ Fri, 05 Jul 2019 04:01:34: 2000000 INFO @ Fri, 05 Jul 2019 04:01:36: 2000000 INFO @ Fri, 05 Jul 2019 04:01:39: 2000000 INFO @ Fri, 05 Jul 2019 04:01:41: 3000000 INFO @ Fri, 05 Jul 2019 04:01:43: 3000000 INFO @ Fri, 05 Jul 2019 04:01:49: 3000000 INFO @ Fri, 05 Jul 2019 04:01:49: 4000000 INFO @ Fri, 05 Jul 2019 04:01:52: 4000000 INFO @ Fri, 05 Jul 2019 04:01:58: 5000000 INFO @ Fri, 05 Jul 2019 04:01:59: 4000000 INFO @ Fri, 05 Jul 2019 04:02:00: 5000000 INFO @ Fri, 05 Jul 2019 04:02:06: 6000000 INFO @ Fri, 05 Jul 2019 04:02:08: 6000000 INFO @ Fri, 05 Jul 2019 04:02:09: 5000000 INFO @ Fri, 05 Jul 2019 04:02:13: 7000000 INFO @ Fri, 05 Jul 2019 04:02:15: 7000000 INFO @ Fri, 05 Jul 2019 04:02:19: 6000000 INFO @ Fri, 05 Jul 2019 04:02:21: 8000000 INFO @ Fri, 05 Jul 2019 04:02:22: 8000000 INFO @ Fri, 05 Jul 2019 04:02:28: 9000000 INFO @ Fri, 05 Jul 2019 04:02:28: 7000000 INFO @ Fri, 05 Jul 2019 04:02:30: 9000000 INFO @ Fri, 05 Jul 2019 04:02:35: 10000000 INFO @ Fri, 05 Jul 2019 04:02:37: 10000000 INFO @ Fri, 05 Jul 2019 04:02:38: 8000000 INFO @ Fri, 05 Jul 2019 04:02:43: 11000000 INFO @ Fri, 05 Jul 2019 04:02:44: 11000000 INFO @ Fri, 05 Jul 2019 04:02:48: 9000000 INFO @ Fri, 05 Jul 2019 04:02:50: 12000000 INFO @ Fri, 05 Jul 2019 04:02:52: 12000000 INFO @ Fri, 05 Jul 2019 04:02:57: 13000000 INFO @ Fri, 05 Jul 2019 04:02:58: 10000000 INFO @ Fri, 05 Jul 2019 04:02:59: 13000000 INFO @ Fri, 05 Jul 2019 04:03:04: 14000000 INFO @ Fri, 05 Jul 2019 04:03:06: 14000000 INFO @ Fri, 05 Jul 2019 04:03:08: 11000000 INFO @ Fri, 05 Jul 2019 04:03:11: 15000000 INFO @ Fri, 05 Jul 2019 04:03:13: 15000000 INFO @ Fri, 05 Jul 2019 04:03:17: 12000000 INFO @ Fri, 05 Jul 2019 04:03:19: 16000000 INFO @ Fri, 05 Jul 2019 04:03:21: 16000000 INFO @ Fri, 05 Jul 2019 04:03:26: 17000000 INFO @ Fri, 05 Jul 2019 04:03:26: 13000000 INFO @ Fri, 05 Jul 2019 04:03:28: 17000000 INFO @ Fri, 05 Jul 2019 04:03:33: 18000000 INFO @ Fri, 05 Jul 2019 04:03:35: 18000000 INFO @ Fri, 05 Jul 2019 04:03:36: 14000000 INFO @ Fri, 05 Jul 2019 04:03:41: 19000000 INFO @ Fri, 05 Jul 2019 04:03:43: 19000000 INFO @ Fri, 05 Jul 2019 04:03:45: 15000000 INFO @ Fri, 05 Jul 2019 04:03:49: 20000000 INFO @ Fri, 05 Jul 2019 04:03:49: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:03:49: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:03:49: #1 total tags in treatment: 20020420 INFO @ Fri, 05 Jul 2019 04:03:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:03:49: #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 04:03:50: #1 tags after filtering in treatment: 20020253 INFO @ Fri, 05 Jul 2019 04:03:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:03:50: #1 finished! INFO @ Fri, 05 Jul 2019 04:03:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:03:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:03:51: 20000000 INFO @ Fri, 05 Jul 2019 04:03:51: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:03:51: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:03:51: #1 total tags in treatment: 20020420 INFO @ Fri, 05 Jul 2019 04:03:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:03:51: #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 04:03:51: #1 tags after filtering in treatment: 20020253 INFO @ Fri, 05 Jul 2019 04:03:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:03:51: #1 finished! INFO @ Fri, 05 Jul 2019 04:03:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:03:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:03:52: 16000000 INFO @ Fri, 05 Jul 2019 04:03:54: #2 number of paired peaks: 48592 INFO @ Fri, 05 Jul 2019 04:03:54: start model_add_line... INFO @ Fri, 05 Jul 2019 04:03:54: start X-correlation... INFO @ Fri, 05 Jul 2019 04:03:54: end of X-cor INFO @ Fri, 05 Jul 2019 04:03:54: #2 finished! INFO @ Fri, 05 Jul 2019 04:03:54: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 04:03:54: #2 alternative fragment length(s) may be 1,132,295 bps INFO @ Fri, 05 Jul 2019 04:03:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.05_model.r INFO @ Fri, 05 Jul 2019 04:03:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:03:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:03:56: #2 number of paired peaks: 48592 INFO @ Fri, 05 Jul 2019 04:03:56: start model_add_line... INFO @ Fri, 05 Jul 2019 04:03:56: start X-correlation... INFO @ Fri, 05 Jul 2019 04:03:56: end of X-cor INFO @ Fri, 05 Jul 2019 04:03:56: #2 finished! INFO @ Fri, 05 Jul 2019 04:03:56: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 04:03:56: #2 alternative fragment length(s) may be 1,132,295 bps INFO @ Fri, 05 Jul 2019 04:03:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.20_model.r INFO @ Fri, 05 Jul 2019 04:03:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:03:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:03:59: 17000000 INFO @ Fri, 05 Jul 2019 04:04:06: 18000000 INFO @ Fri, 05 Jul 2019 04:04:13: 19000000 INFO @ Fri, 05 Jul 2019 04:04:21: 20000000 INFO @ Fri, 05 Jul 2019 04:04:21: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:04:21: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:04:21: #1 total tags in treatment: 20020420 INFO @ Fri, 05 Jul 2019 04:04:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:04:21: #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 04:04:22: #1 tags after filtering in treatment: 20020253 INFO @ Fri, 05 Jul 2019 04:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:04:22: #1 finished! INFO @ Fri, 05 Jul 2019 04:04:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:04:26: #2 number of paired peaks: 48592 INFO @ Fri, 05 Jul 2019 04:04:26: start model_add_line... INFO @ Fri, 05 Jul 2019 04:04:26: start X-correlation... INFO @ Fri, 05 Jul 2019 04:04:26: end of X-cor INFO @ Fri, 05 Jul 2019 04:04:26: #2 finished! INFO @ Fri, 05 Jul 2019 04:04:26: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 04:04:26: #2 alternative fragment length(s) may be 1,132,295 bps INFO @ Fri, 05 Jul 2019 04:04:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.10_model.r INFO @ Fri, 05 Jul 2019 04:04:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:04:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:04:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:05:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:05:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:05:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:05:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:05:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.05_summits.bed INFO @ Fri, 05 Jul 2019 04:05:31: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (1069 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:05:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:05:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:05:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.20_summits.bed INFO @ Fri, 05 Jul 2019 04:05:33: Done! pass1 - making usageList (19 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:06:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:06:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:06:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101837/ERX101837.10_summits.bed INFO @ Fri, 05 Jul 2019 04:06:04: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (239 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。