Job ID = 2640703 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,388,237 reads read : 62,776,474 reads written : 31,388,237 reads 0-length : 31,388,237 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: 00:22:53 31388237 reads; of these: 31388237 (100.00%) were unpaired; of these: 766083 (2.44%) aligned 0 times 25772130 (82.11%) aligned exactly 1 time 4850024 (15.45%) aligned >1 times 97.56% overall alignment rate Time searching: 00:22:56 Overall time: 00:22:56 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 16 files... [bam_rmdupse_core] 1786510 / 30622154 = 0.0583 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:59:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.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 18:59:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:59:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:59:14: 1000000 INFO @ Sat, 24 Aug 2019 18:59:21: 2000000 INFO @ Sat, 24 Aug 2019 18:59:28: 3000000 INFO @ Sat, 24 Aug 2019 18:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.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 18:59:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:59:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:59:35: 4000000 INFO @ Sat, 24 Aug 2019 18:59:43: 5000000 INFO @ Sat, 24 Aug 2019 18:59:43: 1000000 INFO @ Sat, 24 Aug 2019 18:59:50: 6000000 INFO @ Sat, 24 Aug 2019 18:59:50: 2000000 INFO @ Sat, 24 Aug 2019 18:59:58: 7000000 INFO @ Sat, 24 Aug 2019 18:59:58: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:00:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.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 19:00:05: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:00:05: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:00:05: 4000000 INFO @ Sat, 24 Aug 2019 19:00:05: 8000000 INFO @ Sat, 24 Aug 2019 19:00:13: 5000000 INFO @ Sat, 24 Aug 2019 19:00:13: 1000000 INFO @ Sat, 24 Aug 2019 19:00:13: 9000000 INFO @ Sat, 24 Aug 2019 19:00:20: 6000000 INFO @ Sat, 24 Aug 2019 19:00:20: 2000000 INFO @ Sat, 24 Aug 2019 19:00:21: 10000000 INFO @ Sat, 24 Aug 2019 19:00:28: 7000000 INFO @ Sat, 24 Aug 2019 19:00:28: 3000000 INFO @ Sat, 24 Aug 2019 19:00:28: 11000000 INFO @ Sat, 24 Aug 2019 19:00:35: 4000000 INFO @ Sat, 24 Aug 2019 19:00:35: 8000000 INFO @ Sat, 24 Aug 2019 19:00:35: 12000000 INFO @ Sat, 24 Aug 2019 19:00:43: 5000000 INFO @ Sat, 24 Aug 2019 19:00:43: 13000000 INFO @ Sat, 24 Aug 2019 19:00:43: 9000000 INFO @ Sat, 24 Aug 2019 19:00:50: 6000000 INFO @ Sat, 24 Aug 2019 19:00:50: 10000000 INFO @ Sat, 24 Aug 2019 19:00:50: 14000000 INFO @ Sat, 24 Aug 2019 19:00:58: 11000000 INFO @ Sat, 24 Aug 2019 19:00:58: 15000000 INFO @ Sat, 24 Aug 2019 19:00:58: 7000000 INFO @ Sat, 24 Aug 2019 19:01:05: 12000000 INFO @ Sat, 24 Aug 2019 19:01:05: 16000000 INFO @ Sat, 24 Aug 2019 19:01:06: 8000000 INFO @ Sat, 24 Aug 2019 19:01:12: 13000000 INFO @ Sat, 24 Aug 2019 19:01:13: 17000000 INFO @ Sat, 24 Aug 2019 19:01:13: 9000000 INFO @ Sat, 24 Aug 2019 19:01:20: 14000000 INFO @ Sat, 24 Aug 2019 19:01:20: 18000000 INFO @ Sat, 24 Aug 2019 19:01:21: 10000000 INFO @ Sat, 24 Aug 2019 19:01:27: 15000000 INFO @ Sat, 24 Aug 2019 19:01:28: 19000000 INFO @ Sat, 24 Aug 2019 19:01:28: 11000000 INFO @ Sat, 24 Aug 2019 19:01:35: 16000000 INFO @ Sat, 24 Aug 2019 19:01:35: 20000000 INFO @ Sat, 24 Aug 2019 19:01:36: 12000000 INFO @ Sat, 24 Aug 2019 19:01:42: 17000000 INFO @ Sat, 24 Aug 2019 19:01:43: 21000000 INFO @ Sat, 24 Aug 2019 19:01:43: 13000000 INFO @ Sat, 24 Aug 2019 19:01:49: 18000000 INFO @ Sat, 24 Aug 2019 19:01:50: 22000000 INFO @ Sat, 24 Aug 2019 19:01:50: 14000000 INFO @ Sat, 24 Aug 2019 19:01:57: 19000000 INFO @ Sat, 24 Aug 2019 19:01:58: 23000000 INFO @ Sat, 24 Aug 2019 19:01:58: 15000000 INFO @ Sat, 24 Aug 2019 19:02:04: 20000000 INFO @ Sat, 24 Aug 2019 19:02:05: 24000000 INFO @ Sat, 24 Aug 2019 19:02:05: 16000000 INFO @ Sat, 24 Aug 2019 19:02:11: 21000000 INFO @ Sat, 24 Aug 2019 19:02:12: 25000000 INFO @ Sat, 24 Aug 2019 19:02:13: 17000000 INFO @ Sat, 24 Aug 2019 19:02:19: 22000000 INFO @ Sat, 24 Aug 2019 19:02:20: 26000000 INFO @ Sat, 24 Aug 2019 19:02:20: 18000000 INFO @ Sat, 24 Aug 2019 19:02:26: 23000000 INFO @ Sat, 24 Aug 2019 19:02:28: 27000000 INFO @ Sat, 24 Aug 2019 19:02:28: 19000000 INFO @ Sat, 24 Aug 2019 19:02:34: 24000000 INFO @ Sat, 24 Aug 2019 19:02:35: 20000000 INFO @ Sat, 24 Aug 2019 19:02:35: 28000000 INFO @ Sat, 24 Aug 2019 19:02:41: 25000000 INFO @ Sat, 24 Aug 2019 19:02:42: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:02:42: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:02:42: #1 total tags in treatment: 28835644 INFO @ Sat, 24 Aug 2019 19:02:42: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:02:42: #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 19:02:43: 21000000 INFO @ Sat, 24 Aug 2019 19:02:43: #1 tags after filtering in treatment: 28835446 INFO @ Sat, 24 Aug 2019 19:02:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:02:43: #1 finished! INFO @ Sat, 24 Aug 2019 19:02:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:02:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:02:48: 26000000 INFO @ Sat, 24 Aug 2019 19:02:50: 22000000 INFO @ Sat, 24 Aug 2019 19:02:51: #2 number of paired peaks: 119473 INFO @ Sat, 24 Aug 2019 19:02:51: start model_add_line... INFO @ Sat, 24 Aug 2019 19:02:52: start X-correlation... INFO @ Sat, 24 Aug 2019 19:02:52: end of X-cor INFO @ Sat, 24 Aug 2019 19:02:52: #2 finished! INFO @ Sat, 24 Aug 2019 19:02:52: #2 predicted fragment length is 237 bps INFO @ Sat, 24 Aug 2019 19:02:52: #2 alternative fragment length(s) may be 4,237 bps INFO @ Sat, 24 Aug 2019 19:02:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.05_model.r INFO @ Sat, 24 Aug 2019 19:02:52: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:02:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:02:56: 27000000 INFO @ Sat, 24 Aug 2019 19:02:57: 23000000 INFO @ Sat, 24 Aug 2019 19:03:03: 28000000 INFO @ Sat, 24 Aug 2019 19:03:04: 24000000 INFO @ Sat, 24 Aug 2019 19:03:10: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:03:10: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:03:10: #1 total tags in treatment: 28835644 INFO @ Sat, 24 Aug 2019 19:03:10: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:03:10: #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 19:03:11: #1 tags after filtering in treatment: 28835446 INFO @ Sat, 24 Aug 2019 19:03:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:03:11: #1 finished! INFO @ Sat, 24 Aug 2019 19:03:11: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:03:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:03:12: 25000000 INFO @ Sat, 24 Aug 2019 19:03:19: #2 number of paired peaks: 119473 INFO @ Sat, 24 Aug 2019 19:03:19: start model_add_line... INFO @ Sat, 24 Aug 2019 19:03:19: 26000000 INFO @ Sat, 24 Aug 2019 19:03:19: start X-correlation... INFO @ Sat, 24 Aug 2019 19:03:19: end of X-cor INFO @ Sat, 24 Aug 2019 19:03:19: #2 finished! INFO @ Sat, 24 Aug 2019 19:03:19: #2 predicted fragment length is 237 bps INFO @ Sat, 24 Aug 2019 19:03:19: #2 alternative fragment length(s) may be 4,237 bps INFO @ Sat, 24 Aug 2019 19:03:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.10_model.r INFO @ Sat, 24 Aug 2019 19:03:19: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:03:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:03:26: 27000000 INFO @ Sat, 24 Aug 2019 19:03:34: 28000000 INFO @ Sat, 24 Aug 2019 19:03:40: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:03:40: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:03:40: #1 total tags in treatment: 28835644 INFO @ Sat, 24 Aug 2019 19:03:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:03:40: #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 19:03:41: #1 tags after filtering in treatment: 28835446 INFO @ Sat, 24 Aug 2019 19:03:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:03:41: #1 finished! INFO @ Sat, 24 Aug 2019 19:03:41: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:03:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:03:49: #2 number of paired peaks: 119473 INFO @ Sat, 24 Aug 2019 19:03:49: start model_add_line... INFO @ Sat, 24 Aug 2019 19:03:50: start X-correlation... INFO @ Sat, 24 Aug 2019 19:03:50: end of X-cor INFO @ Sat, 24 Aug 2019 19:03:50: #2 finished! INFO @ Sat, 24 Aug 2019 19:03:50: #2 predicted fragment length is 237 bps INFO @ Sat, 24 Aug 2019 19:03:50: #2 alternative fragment length(s) may be 4,237 bps INFO @ Sat, 24 Aug 2019 19:03:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.20_model.r INFO @ Sat, 24 Aug 2019 19:03:50: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:03:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:04:27: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:04:54: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:05:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:05:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:05:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.05_summits.bed INFO @ Sat, 24 Aug 2019 19:05:19: Done! pass1 - making usageList (133 chroms): 12 millis pass2 - checking and writing primary data (36388 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:05:25: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:05:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:05:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:05:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.10_summits.bed INFO @ Sat, 24 Aug 2019 19:05:45: Done! pass1 - making usageList (86 chroms): 8 millis pass2 - checking and writing primary data (19136 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:06:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:06:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:06:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375060/SRX5375060.20_summits.bed INFO @ Sat, 24 Aug 2019 19:06:19: Done! pass1 - making usageList (44 chroms): 4 millis pass2 - checking and writing primary data (6111 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。