Job ID = 2640555 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,570,115 reads read : 21,140,230 reads written : 10,570,115 reads 0-length : 10,570,115 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: 00:00:00 Multiseed full-index search: 00:08:48 10570115 reads; of these: 10570115 (100.00%) were unpaired; of these: 619189 (5.86%) aligned 0 times 7475549 (70.72%) aligned exactly 1 time 2475377 (23.42%) aligned >1 times 94.14% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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] 454622 / 9950926 = 0.0457 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:47:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.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 17:47:59: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:47:59: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:48:08: 1000000 INFO @ Sat, 24 Aug 2019 17:48:16: 2000000 INFO @ Sat, 24 Aug 2019 17:48:25: 3000000 INFO @ Sat, 24 Aug 2019 17:48:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.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 17:48:28: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:48:28: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:48:34: 4000000 INFO @ Sat, 24 Aug 2019 17:48:36: 1000000 INFO @ Sat, 24 Aug 2019 17:48:44: 5000000 INFO @ Sat, 24 Aug 2019 17:48:44: 2000000 INFO @ Sat, 24 Aug 2019 17:48:52: 3000000 INFO @ Sat, 24 Aug 2019 17:48:53: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.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 17:48:58: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:48:58: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:49:01: 4000000 INFO @ Sat, 24 Aug 2019 17:49:02: 7000000 INFO @ Sat, 24 Aug 2019 17:49:07: 1000000 INFO @ Sat, 24 Aug 2019 17:49:09: 5000000 INFO @ Sat, 24 Aug 2019 17:49:11: 8000000 INFO @ Sat, 24 Aug 2019 17:49:17: 2000000 INFO @ Sat, 24 Aug 2019 17:49:18: 6000000 INFO @ Sat, 24 Aug 2019 17:49:21: 9000000 INFO @ Sat, 24 Aug 2019 17:49:26: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:49:26: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:49:26: #1 total tags in treatment: 9496304 INFO @ Sat, 24 Aug 2019 17:49:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:49:26: #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 17:49:26: 3000000 INFO @ Sat, 24 Aug 2019 17:49:26: #1 tags after filtering in treatment: 9496071 INFO @ Sat, 24 Aug 2019 17:49:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:49:26: #1 finished! INFO @ Sat, 24 Aug 2019 17:49:26: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:49:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:49:27: 7000000 INFO @ Sat, 24 Aug 2019 17:49:28: #2 number of paired peaks: 28421 INFO @ Sat, 24 Aug 2019 17:49:28: start model_add_line... INFO @ Sat, 24 Aug 2019 17:49:28: start X-correlation... INFO @ Sat, 24 Aug 2019 17:49:28: end of X-cor INFO @ Sat, 24 Aug 2019 17:49:28: #2 finished! INFO @ Sat, 24 Aug 2019 17:49:28: #2 predicted fragment length is 172 bps INFO @ Sat, 24 Aug 2019 17:49:28: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 24 Aug 2019 17:49:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.05_model.r INFO @ Sat, 24 Aug 2019 17:49:28: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:49:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:49:35: 4000000 INFO @ Sat, 24 Aug 2019 17:49:35: 8000000 INFO @ Sat, 24 Aug 2019 17:49:44: 9000000 INFO @ Sat, 24 Aug 2019 17:49:44: 5000000 INFO @ Sat, 24 Aug 2019 17:49:48: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:49:48: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:49:48: #1 total tags in treatment: 9496304 INFO @ Sat, 24 Aug 2019 17:49:48: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:49:48: #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 17:49:49: #1 tags after filtering in treatment: 9496071 INFO @ Sat, 24 Aug 2019 17:49:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:49:49: #1 finished! INFO @ Sat, 24 Aug 2019 17:49:49: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:49:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:49:51: #2 number of paired peaks: 28421 INFO @ Sat, 24 Aug 2019 17:49:51: start model_add_line... INFO @ Sat, 24 Aug 2019 17:49:51: start X-correlation... INFO @ Sat, 24 Aug 2019 17:49:51: end of X-cor INFO @ Sat, 24 Aug 2019 17:49:51: #2 finished! INFO @ Sat, 24 Aug 2019 17:49:51: #2 predicted fragment length is 172 bps INFO @ Sat, 24 Aug 2019 17:49:51: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 24 Aug 2019 17:49:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.10_model.r INFO @ Sat, 24 Aug 2019 17:49:51: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:49:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:49:53: 6000000 INFO @ Sat, 24 Aug 2019 17:49:59: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:50:01: 7000000 INFO @ Sat, 24 Aug 2019 17:50:10: 8000000 INFO @ Sat, 24 Aug 2019 17:50:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:50:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:50:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.05_summits.bed INFO @ Sat, 24 Aug 2019 17:50:15: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (2709 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:50:19: 9000000 INFO @ Sat, 24 Aug 2019 17:50:22: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:50:23: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:50:23: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:50:23: #1 total tags in treatment: 9496304 INFO @ Sat, 24 Aug 2019 17:50:23: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:50:23: #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 17:50:24: #1 tags after filtering in treatment: 9496071 INFO @ Sat, 24 Aug 2019 17:50:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:50:24: #1 finished! INFO @ Sat, 24 Aug 2019 17:50:24: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:50:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:50:26: #2 number of paired peaks: 28421 INFO @ Sat, 24 Aug 2019 17:50:26: start model_add_line... INFO @ Sat, 24 Aug 2019 17:50:26: start X-correlation... INFO @ Sat, 24 Aug 2019 17:50:26: end of X-cor INFO @ Sat, 24 Aug 2019 17:50:26: #2 finished! INFO @ Sat, 24 Aug 2019 17:50:26: #2 predicted fragment length is 172 bps INFO @ Sat, 24 Aug 2019 17:50:26: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 24 Aug 2019 17:50:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.20_model.r INFO @ Sat, 24 Aug 2019 17:50:26: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:50:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:50:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:50:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:50:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.10_summits.bed INFO @ Sat, 24 Aug 2019 17:50:38: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (662 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:50:57: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:51:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:51:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:51:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375009/SRX5375009.20_summits.bed INFO @ Sat, 24 Aug 2019 17:51:37: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (209 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。