Job ID = 2640571 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,607,180 reads read : 41,214,360 reads written : 20,607,180 reads 0-length : 20,607,180 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:13:28 20607180 reads; of these: 20607180 (100.00%) were unpaired; of these: 1451990 (7.05%) aligned 0 times 15605168 (75.73%) aligned exactly 1 time 3550022 (17.23%) aligned >1 times 92.95% overall alignment rate Time searching: 00:13:31 Overall time: 00:13:31 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] 1881685 / 19155190 = 0.0982 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:05:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.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 @ Sat, 24 Aug 2019 18:05:00: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:05:00: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:05:08: 1000000 INFO @ Sat, 24 Aug 2019 18:05:15: 2000000 INFO @ Sat, 24 Aug 2019 18:05:23: 3000000 INFO @ Sat, 24 Aug 2019 18:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.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 @ Sat, 24 Aug 2019 18:05:29: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:05:29: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:05:30: 4000000 INFO @ Sat, 24 Aug 2019 18:05:37: 1000000 INFO @ Sat, 24 Aug 2019 18:05:37: 5000000 INFO @ Sat, 24 Aug 2019 18:05:44: 2000000 INFO @ Sat, 24 Aug 2019 18:05:44: 6000000 INFO @ Sat, 24 Aug 2019 18:05:51: 3000000 INFO @ Sat, 24 Aug 2019 18:05:52: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:05:58: 4000000 INFO @ Sat, 24 Aug 2019 18:05:59: 8000000 INFO @ Sat, 24 Aug 2019 18:05:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.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 @ Sat, 24 Aug 2019 18:05:59: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:05:59: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:06:05: 5000000 INFO @ Sat, 24 Aug 2019 18:06:07: 9000000 INFO @ Sat, 24 Aug 2019 18:06:07: 1000000 INFO @ Sat, 24 Aug 2019 18:06:12: 6000000 INFO @ Sat, 24 Aug 2019 18:06:14: 10000000 INFO @ Sat, 24 Aug 2019 18:06:15: 2000000 INFO @ Sat, 24 Aug 2019 18:06:19: 7000000 INFO @ Sat, 24 Aug 2019 18:06:21: 11000000 INFO @ Sat, 24 Aug 2019 18:06:22: 3000000 INFO @ Sat, 24 Aug 2019 18:06:26: 8000000 INFO @ Sat, 24 Aug 2019 18:06:29: 12000000 INFO @ Sat, 24 Aug 2019 18:06:29: 4000000 INFO @ Sat, 24 Aug 2019 18:06:33: 9000000 INFO @ Sat, 24 Aug 2019 18:06:36: 13000000 INFO @ Sat, 24 Aug 2019 18:06:36: 5000000 INFO @ Sat, 24 Aug 2019 18:06:40: 10000000 INFO @ Sat, 24 Aug 2019 18:06:44: 6000000 INFO @ Sat, 24 Aug 2019 18:06:44: 14000000 INFO @ Sat, 24 Aug 2019 18:06:47: 11000000 INFO @ Sat, 24 Aug 2019 18:06:51: 7000000 INFO @ Sat, 24 Aug 2019 18:06:51: 15000000 INFO @ Sat, 24 Aug 2019 18:06:54: 12000000 INFO @ Sat, 24 Aug 2019 18:06:58: 8000000 INFO @ Sat, 24 Aug 2019 18:06:59: 16000000 INFO @ Sat, 24 Aug 2019 18:07:01: 13000000 INFO @ Sat, 24 Aug 2019 18:07:06: 9000000 INFO @ Sat, 24 Aug 2019 18:07:07: 17000000 INFO @ Sat, 24 Aug 2019 18:07:09: 14000000 INFO @ Sat, 24 Aug 2019 18:07:09: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:07:09: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:07:09: #1 total tags in treatment: 17273505 INFO @ Sat, 24 Aug 2019 18:07:09: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:07:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:07:09: #1 tags after filtering in treatment: 17273272 INFO @ Sat, 24 Aug 2019 18:07:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:07:09: #1 finished! INFO @ Sat, 24 Aug 2019 18:07:09: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:07:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:07:13: 10000000 INFO @ Sat, 24 Aug 2019 18:07:15: #2 number of paired peaks: 91072 INFO @ Sat, 24 Aug 2019 18:07:15: start model_add_line... INFO @ Sat, 24 Aug 2019 18:07:15: start X-correlation... INFO @ Sat, 24 Aug 2019 18:07:15: end of X-cor INFO @ Sat, 24 Aug 2019 18:07:15: #2 finished! INFO @ Sat, 24 Aug 2019 18:07:15: #2 predicted fragment length is 212 bps INFO @ Sat, 24 Aug 2019 18:07:15: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 24 Aug 2019 18:07:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.05_model.r INFO @ Sat, 24 Aug 2019 18:07:15: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:07:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:07:16: 15000000 INFO @ Sat, 24 Aug 2019 18:07:20: 11000000 INFO @ Sat, 24 Aug 2019 18:07:23: 16000000 INFO @ Sat, 24 Aug 2019 18:07:27: 12000000 INFO @ Sat, 24 Aug 2019 18:07:30: 17000000 INFO @ Sat, 24 Aug 2019 18:07:32: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:07:32: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:07:32: #1 total tags in treatment: 17273505 INFO @ Sat, 24 Aug 2019 18:07:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:07:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:07:32: #1 tags after filtering in treatment: 17273272 INFO @ Sat, 24 Aug 2019 18:07:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:07:32: #1 finished! INFO @ Sat, 24 Aug 2019 18:07:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:07:35: 13000000 INFO @ Sat, 24 Aug 2019 18:07:38: #2 number of paired peaks: 91072 INFO @ Sat, 24 Aug 2019 18:07:38: start model_add_line... INFO @ Sat, 24 Aug 2019 18:07:38: start X-correlation... INFO @ Sat, 24 Aug 2019 18:07:38: end of X-cor INFO @ Sat, 24 Aug 2019 18:07:38: #2 finished! INFO @ Sat, 24 Aug 2019 18:07:38: #2 predicted fragment length is 212 bps INFO @ Sat, 24 Aug 2019 18:07:38: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 24 Aug 2019 18:07:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.10_model.r INFO @ Sat, 24 Aug 2019 18:07:38: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:07:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:07:42: 14000000 INFO @ Sat, 24 Aug 2019 18:07:49: 15000000 INFO @ Sat, 24 Aug 2019 18:07:56: 16000000 INFO @ Sat, 24 Aug 2019 18:08:04: 17000000 INFO @ Sat, 24 Aug 2019 18:08:06: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:08:06: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:08:06: #1 total tags in treatment: 17273505 INFO @ Sat, 24 Aug 2019 18:08:06: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:08:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:08:06: #1 tags after filtering in treatment: 17273272 INFO @ Sat, 24 Aug 2019 18:08:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:08:06: #1 finished! INFO @ Sat, 24 Aug 2019 18:08:06: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:08:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:08:12: #2 number of paired peaks: 91072 INFO @ Sat, 24 Aug 2019 18:08:12: start model_add_line... INFO @ Sat, 24 Aug 2019 18:08:12: start X-correlation... INFO @ Sat, 24 Aug 2019 18:08:12: end of X-cor INFO @ Sat, 24 Aug 2019 18:08:12: #2 finished! INFO @ Sat, 24 Aug 2019 18:08:12: #2 predicted fragment length is 212 bps INFO @ Sat, 24 Aug 2019 18:08:12: #2 alternative fragment length(s) may be 212 bps INFO @ Sat, 24 Aug 2019 18:08:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.20_model.r INFO @ Sat, 24 Aug 2019 18:08:12: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:08:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:08:13: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:08:34: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:08:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:08:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:08:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.05_summits.bed INFO @ Sat, 24 Aug 2019 18:08:44: Done! pass1 - making usageList (67 chroms): 5 millis pass2 - checking and writing primary data (9243 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:09:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:09:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:09:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.10_summits.bed INFO @ Sat, 24 Aug 2019 18:09:03: Done! pass1 - making usageList (40 chroms): 3 millis pass2 - checking and writing primary data (3725 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:09:10: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:09:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:09:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:09:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375016/SRX5375016.20_summits.bed INFO @ Sat, 24 Aug 2019 18:09:40: Done! pass1 - making usageList (28 chroms): 2 millis pass2 - checking and writing primary data (893 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。