Job ID = 2640723 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,991,081 reads read : 16,991,081 reads written : 16,991,081 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1302417.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:01 16991081 reads; of these: 16991081 (100.00%) were unpaired; of these: 1123726 (6.61%) aligned 0 times 11992603 (70.58%) aligned exactly 1 time 3874752 (22.80%) aligned >1 times 93.39% overall alignment rate Time searching: 00:09:03 Overall time: 00:09:03 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] 584369 / 15867355 = 0.0368 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:41:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.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 18:41:18: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:41:18: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:41:26: 1000000 INFO @ Sat, 24 Aug 2019 18:41:35: 2000000 INFO @ Sat, 24 Aug 2019 18:41:43: 3000000 INFO @ Sat, 24 Aug 2019 18:41:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.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 18:41:48: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:41:48: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:41:51: 4000000 INFO @ Sat, 24 Aug 2019 18:41:56: 1000000 INFO @ Sat, 24 Aug 2019 18:41:59: 5000000 INFO @ Sat, 24 Aug 2019 18:42:04: 2000000 INFO @ Sat, 24 Aug 2019 18:42:07: 6000000 INFO @ Sat, 24 Aug 2019 18:42:13: 3000000 INFO @ Sat, 24 Aug 2019 18:42:14: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:42:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.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 18:42:18: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:42:18: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:42:21: 8000000 INFO @ Sat, 24 Aug 2019 18:42:21: 4000000 INFO @ Sat, 24 Aug 2019 18:42:25: 1000000 INFO @ Sat, 24 Aug 2019 18:42:28: 9000000 INFO @ Sat, 24 Aug 2019 18:42:29: 5000000 INFO @ Sat, 24 Aug 2019 18:42:33: 2000000 INFO @ Sat, 24 Aug 2019 18:42:35: 10000000 INFO @ Sat, 24 Aug 2019 18:42:37: 6000000 INFO @ Sat, 24 Aug 2019 18:42:40: 3000000 INFO @ Sat, 24 Aug 2019 18:42:42: 11000000 INFO @ Sat, 24 Aug 2019 18:42:45: 7000000 INFO @ Sat, 24 Aug 2019 18:42:47: 4000000 INFO @ Sat, 24 Aug 2019 18:42:49: 12000000 INFO @ Sat, 24 Aug 2019 18:42:53: 8000000 INFO @ Sat, 24 Aug 2019 18:42:54: 5000000 INFO @ Sat, 24 Aug 2019 18:42:56: 13000000 INFO @ Sat, 24 Aug 2019 18:43:01: 9000000 INFO @ Sat, 24 Aug 2019 18:43:01: 6000000 INFO @ Sat, 24 Aug 2019 18:43:03: 14000000 INFO @ Sat, 24 Aug 2019 18:43:08: 7000000 INFO @ Sat, 24 Aug 2019 18:43:09: 10000000 INFO @ Sat, 24 Aug 2019 18:43:10: 15000000 INFO @ Sat, 24 Aug 2019 18:43:13: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 18:43:13: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 18:43:13: #1 total tags in treatment: 15282986 INFO @ Sat, 24 Aug 2019 18:43:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:43:13: #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 18:43:13: #1 tags after filtering in treatment: 15282801 INFO @ Sat, 24 Aug 2019 18:43:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:43:13: #1 finished! INFO @ Sat, 24 Aug 2019 18:43:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:43:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:43:15: 8000000 INFO @ Sat, 24 Aug 2019 18:43:16: #2 number of paired peaks: 35465 INFO @ Sat, 24 Aug 2019 18:43:16: start model_add_line... INFO @ Sat, 24 Aug 2019 18:43:16: start X-correlation... INFO @ Sat, 24 Aug 2019 18:43:16: end of X-cor INFO @ Sat, 24 Aug 2019 18:43:16: #2 finished! INFO @ Sat, 24 Aug 2019 18:43:16: #2 predicted fragment length is 139 bps INFO @ Sat, 24 Aug 2019 18:43:16: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 24 Aug 2019 18:43:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.05_model.r INFO @ Sat, 24 Aug 2019 18:43:16: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:43:17: 11000000 INFO @ Sat, 24 Aug 2019 18:43:22: 9000000 INFO @ Sat, 24 Aug 2019 18:43:25: 12000000 INFO @ Sat, 24 Aug 2019 18:43:29: 10000000 INFO @ Sat, 24 Aug 2019 18:43:34: 13000000 INFO @ Sat, 24 Aug 2019 18:43:36: 11000000 INFO @ Sat, 24 Aug 2019 18:43:42: 14000000 INFO @ Sat, 24 Aug 2019 18:43:43: 12000000 INFO @ Sat, 24 Aug 2019 18:43:50: 15000000 INFO @ Sat, 24 Aug 2019 18:43:51: 13000000 INFO @ Sat, 24 Aug 2019 18:43:53: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 18:43:53: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 18:43:53: #1 total tags in treatment: 15282986 INFO @ Sat, 24 Aug 2019 18:43:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:43:53: #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 18:43:53: #1 tags after filtering in treatment: 15282801 INFO @ Sat, 24 Aug 2019 18:43:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:43:53: #1 finished! INFO @ Sat, 24 Aug 2019 18:43:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:43:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:43:56: #2 number of paired peaks: 35465 INFO @ Sat, 24 Aug 2019 18:43:56: start model_add_line... INFO @ Sat, 24 Aug 2019 18:43:56: start X-correlation... INFO @ Sat, 24 Aug 2019 18:43:56: end of X-cor INFO @ Sat, 24 Aug 2019 18:43:56: #2 finished! INFO @ Sat, 24 Aug 2019 18:43:56: #2 predicted fragment length is 139 bps INFO @ Sat, 24 Aug 2019 18:43:56: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 24 Aug 2019 18:43:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.10_model.r INFO @ Sat, 24 Aug 2019 18:43:56: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:43:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:43:58: 14000000 INFO @ Sat, 24 Aug 2019 18:44:05: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:44:05: 15000000 INFO @ Sat, 24 Aug 2019 18:44:07: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 18:44:07: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 18:44:07: #1 total tags in treatment: 15282986 INFO @ Sat, 24 Aug 2019 18:44:07: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:44:07: #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 18:44:08: #1 tags after filtering in treatment: 15282801 INFO @ Sat, 24 Aug 2019 18:44:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:44:08: #1 finished! INFO @ Sat, 24 Aug 2019 18:44:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:44:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:44:11: #2 number of paired peaks: 35465 INFO @ Sat, 24 Aug 2019 18:44:11: start model_add_line... INFO @ Sat, 24 Aug 2019 18:44:11: start X-correlation... INFO @ Sat, 24 Aug 2019 18:44:11: end of X-cor INFO @ Sat, 24 Aug 2019 18:44:11: #2 finished! INFO @ Sat, 24 Aug 2019 18:44:11: #2 predicted fragment length is 139 bps INFO @ Sat, 24 Aug 2019 18:44:11: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 24 Aug 2019 18:44:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.20_model.r INFO @ Sat, 24 Aug 2019 18:44:11: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:44:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:44:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:44:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:44:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.05_summits.bed INFO @ Sat, 24 Aug 2019 18:44:29: Done! pass1 - making usageList (77 chroms): 7 millis pass2 - checking and writing primary data (17855 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:44:45: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:44:59: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:45:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:45:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:45:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.10_summits.bed INFO @ Sat, 24 Aug 2019 18:45:10: Done! pass1 - making usageList (49 chroms): 3 millis pass2 - checking and writing primary data (6028 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX555167/SRX555167.20_summits.bed INFO @ Sat, 24 Aug 2019 18:45:23: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (1427 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。