Job ID = 2640498 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,356,628 reads read : 56,713,256 reads written : 28,356,628 reads 0-length : 28,356,628 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: 00:00:02 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:24:34 28356628 reads; of these: 28356628 (100.00%) were unpaired; of these: 820842 (2.89%) aligned 0 times 20381366 (71.88%) aligned exactly 1 time 7154420 (25.23%) aligned >1 times 97.11% overall alignment rate Time searching: 00:24:39 Overall time: 00:24:39 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 12 files... [bam_rmdupse_core] 4050378 / 27535786 = 0.1471 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:02:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.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 18:02:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:02:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:02:40: 1000000 INFO @ Sat, 24 Aug 2019 18:02:47: 2000000 INFO @ Sat, 24 Aug 2019 18:02:53: 3000000 INFO @ Sat, 24 Aug 2019 18:03:00: 4000000 INFO @ Sat, 24 Aug 2019 18:03:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.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 18:03:02: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:03:02: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:03:07: 5000000 INFO @ Sat, 24 Aug 2019 18:03:11: 1000000 INFO @ Sat, 24 Aug 2019 18:03:13: 6000000 INFO @ Sat, 24 Aug 2019 18:03:19: 2000000 INFO @ Sat, 24 Aug 2019 18:03:20: 7000000 INFO @ Sat, 24 Aug 2019 18:03:26: 8000000 INFO @ Sat, 24 Aug 2019 18:03:27: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:03:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.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 18:03:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:03:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:03:33: 9000000 INFO @ Sat, 24 Aug 2019 18:03:35: 4000000 INFO @ Sat, 24 Aug 2019 18:03:40: 10000000 INFO @ Sat, 24 Aug 2019 18:03:41: 1000000 INFO @ Sat, 24 Aug 2019 18:03:44: 5000000 INFO @ Sat, 24 Aug 2019 18:03:46: 11000000 INFO @ Sat, 24 Aug 2019 18:03:50: 2000000 INFO @ Sat, 24 Aug 2019 18:03:52: 6000000 INFO @ Sat, 24 Aug 2019 18:03:53: 12000000 INFO @ Sat, 24 Aug 2019 18:03:58: 3000000 INFO @ Sat, 24 Aug 2019 18:03:59: 13000000 INFO @ Sat, 24 Aug 2019 18:04:00: 7000000 INFO @ Sat, 24 Aug 2019 18:04:06: 14000000 INFO @ Sat, 24 Aug 2019 18:04:07: 4000000 INFO @ Sat, 24 Aug 2019 18:04:08: 8000000 INFO @ Sat, 24 Aug 2019 18:04:13: 15000000 INFO @ Sat, 24 Aug 2019 18:04:15: 5000000 INFO @ Sat, 24 Aug 2019 18:04:16: 9000000 INFO @ Sat, 24 Aug 2019 18:04:19: 16000000 INFO @ Sat, 24 Aug 2019 18:04:23: 6000000 INFO @ Sat, 24 Aug 2019 18:04:24: 10000000 INFO @ Sat, 24 Aug 2019 18:04:26: 17000000 INFO @ Sat, 24 Aug 2019 18:04:31: 11000000 INFO @ Sat, 24 Aug 2019 18:04:31: 7000000 INFO @ Sat, 24 Aug 2019 18:04:32: 18000000 INFO @ Sat, 24 Aug 2019 18:04:39: 19000000 INFO @ Sat, 24 Aug 2019 18:04:39: 12000000 INFO @ Sat, 24 Aug 2019 18:04:40: 8000000 INFO @ Sat, 24 Aug 2019 18:04:45: 20000000 INFO @ Sat, 24 Aug 2019 18:04:47: 13000000 INFO @ Sat, 24 Aug 2019 18:04:48: 9000000 INFO @ Sat, 24 Aug 2019 18:04:52: 21000000 INFO @ Sat, 24 Aug 2019 18:04:55: 14000000 INFO @ Sat, 24 Aug 2019 18:04:56: 10000000 INFO @ Sat, 24 Aug 2019 18:04:58: 22000000 INFO @ Sat, 24 Aug 2019 18:05:02: 15000000 INFO @ Sat, 24 Aug 2019 18:05:04: 11000000 INFO @ Sat, 24 Aug 2019 18:05:05: 23000000 INFO @ Sat, 24 Aug 2019 18:05:09: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:05:09: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:05:09: #1 total tags in treatment: 23485408 INFO @ Sat, 24 Aug 2019 18:05:09: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:05:09: #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 18:05:09: #1 tags after filtering in treatment: 23485266 INFO @ Sat, 24 Aug 2019 18:05:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:05:09: #1 finished! INFO @ Sat, 24 Aug 2019 18:05:09: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:05:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:05:10: 16000000 INFO @ Sat, 24 Aug 2019 18:05:12: 12000000 INFO @ Sat, 24 Aug 2019 18:05:12: #2 number of paired peaks: 11321 INFO @ Sat, 24 Aug 2019 18:05:12: start model_add_line... INFO @ Sat, 24 Aug 2019 18:05:13: start X-correlation... INFO @ Sat, 24 Aug 2019 18:05:13: end of X-cor INFO @ Sat, 24 Aug 2019 18:05:13: #2 finished! INFO @ Sat, 24 Aug 2019 18:05:13: #2 predicted fragment length is 126 bps INFO @ Sat, 24 Aug 2019 18:05:13: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 24 Aug 2019 18:05:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.05_model.r INFO @ Sat, 24 Aug 2019 18:05:13: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:05:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:05:18: 17000000 INFO @ Sat, 24 Aug 2019 18:05:20: 13000000 INFO @ Sat, 24 Aug 2019 18:05:25: 18000000 INFO @ Sat, 24 Aug 2019 18:05:28: 14000000 INFO @ Sat, 24 Aug 2019 18:05:33: 19000000 INFO @ Sat, 24 Aug 2019 18:05:36: 15000000 INFO @ Sat, 24 Aug 2019 18:05:41: 20000000 INFO @ Sat, 24 Aug 2019 18:05:45: 16000000 INFO @ Sat, 24 Aug 2019 18:05:48: 21000000 INFO @ Sat, 24 Aug 2019 18:05:53: 17000000 INFO @ Sat, 24 Aug 2019 18:05:56: 22000000 INFO @ Sat, 24 Aug 2019 18:06:01: 18000000 INFO @ Sat, 24 Aug 2019 18:06:04: 23000000 INFO @ Sat, 24 Aug 2019 18:06:08: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:06:08: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:06:08: #1 total tags in treatment: 23485408 INFO @ Sat, 24 Aug 2019 18:06:08: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:06:08: #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 18:06:08: #1 tags after filtering in treatment: 23485266 INFO @ Sat, 24 Aug 2019 18:06:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:06:08: #1 finished! INFO @ Sat, 24 Aug 2019 18:06:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:06:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:06:10: 19000000 INFO @ Sat, 24 Aug 2019 18:06:11: #2 number of paired peaks: 11321 INFO @ Sat, 24 Aug 2019 18:06:11: start model_add_line... INFO @ Sat, 24 Aug 2019 18:06:12: start X-correlation... INFO @ Sat, 24 Aug 2019 18:06:12: end of X-cor INFO @ Sat, 24 Aug 2019 18:06:12: #2 finished! INFO @ Sat, 24 Aug 2019 18:06:12: #2 predicted fragment length is 126 bps INFO @ Sat, 24 Aug 2019 18:06:12: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 24 Aug 2019 18:06:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.10_model.r INFO @ Sat, 24 Aug 2019 18:06:12: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:06:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:06:18: 20000000 INFO @ Sat, 24 Aug 2019 18:06:26: 21000000 INFO @ Sat, 24 Aug 2019 18:06:27: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:06:34: 22000000 INFO @ Sat, 24 Aug 2019 18:06:42: 23000000 INFO @ Sat, 24 Aug 2019 18:06:47: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:06:47: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:06:47: #1 total tags in treatment: 23485408 INFO @ Sat, 24 Aug 2019 18:06:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:06:47: #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 18:06:47: #1 tags after filtering in treatment: 23485266 INFO @ Sat, 24 Aug 2019 18:06:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:06:47: #1 finished! INFO @ Sat, 24 Aug 2019 18:06:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:06:50: #2 number of paired peaks: 11321 INFO @ Sat, 24 Aug 2019 18:06:50: start model_add_line... INFO @ Sat, 24 Aug 2019 18:06:50: start X-correlation... INFO @ Sat, 24 Aug 2019 18:06:50: end of X-cor INFO @ Sat, 24 Aug 2019 18:06:50: #2 finished! INFO @ Sat, 24 Aug 2019 18:06:50: #2 predicted fragment length is 126 bps INFO @ Sat, 24 Aug 2019 18:06:50: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 24 Aug 2019 18:06:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.20_model.r INFO @ Sat, 24 Aug 2019 18:06:50: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:06:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:07:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:07:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:07:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.05_summits.bed INFO @ Sat, 24 Aug 2019 18:07:06: Done! pass1 - making usageList (61 chroms): 2 millis pass2 - checking and writing primary data (3723 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:07:26: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:08:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:08:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:08:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.10_summits.bed INFO @ Sat, 24 Aug 2019 18:08:05: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (1701 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:08:05: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:08:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:08:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:08:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374999/SRX5374999.20_summits.bed INFO @ Sat, 24 Aug 2019 18:08:45: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (771 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。