Job ID = 2002160 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,632,543 reads read : 15,632,543 reads written : 15,632,543 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR458091.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: 00:00:14 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:14 15632543 reads; of these: 15632543 (100.00%) were unpaired; of these: 3188870 (20.40%) aligned 0 times 9726276 (62.22%) aligned exactly 1 time 2717397 (17.38%) aligned >1 times 79.60% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:31 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_rmdupse_core] 2914446 / 12443673 = 0.2342 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 10:47:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.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 @ Fri, 05 Jul 2019 10:47:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:47:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:47:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.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 @ Fri, 05 Jul 2019 10:47:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:47:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:47:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.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 @ Fri, 05 Jul 2019 10:47:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:47:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:47:11: 1000000 INFO @ Fri, 05 Jul 2019 10:47:11: 1000000 INFO @ Fri, 05 Jul 2019 10:47:12: 1000000 INFO @ Fri, 05 Jul 2019 10:47:18: 2000000 INFO @ Fri, 05 Jul 2019 10:47:19: 2000000 INFO @ Fri, 05 Jul 2019 10:47:19: 2000000 INFO @ Fri, 05 Jul 2019 10:47:25: 3000000 INFO @ Fri, 05 Jul 2019 10:47:27: 3000000 INFO @ Fri, 05 Jul 2019 10:47:27: 3000000 INFO @ Fri, 05 Jul 2019 10:47:33: 4000000 INFO @ Fri, 05 Jul 2019 10:47:34: 4000000 INFO @ Fri, 05 Jul 2019 10:47:35: 4000000 INFO @ Fri, 05 Jul 2019 10:47:40: 5000000 INFO @ Fri, 05 Jul 2019 10:47:42: 5000000 INFO @ Fri, 05 Jul 2019 10:47:42: 5000000 INFO @ Fri, 05 Jul 2019 10:47:47: 6000000 INFO @ Fri, 05 Jul 2019 10:47:49: 6000000 INFO @ Fri, 05 Jul 2019 10:47:50: 6000000 INFO @ Fri, 05 Jul 2019 10:47:53: 7000000 INFO @ Fri, 05 Jul 2019 10:47:55: 7000000 INFO @ Fri, 05 Jul 2019 10:47:58: 7000000 INFO @ Fri, 05 Jul 2019 10:48:00: 8000000 INFO @ Fri, 05 Jul 2019 10:48:02: 8000000 INFO @ Fri, 05 Jul 2019 10:48:05: 8000000 INFO @ Fri, 05 Jul 2019 10:48:06: 9000000 INFO @ Fri, 05 Jul 2019 10:48:08: 9000000 INFO @ Fri, 05 Jul 2019 10:48:10: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:48:10: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:48:10: #1 total tags in treatment: 9529227 INFO @ Fri, 05 Jul 2019 10:48:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:48:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:48:10: #1 tags after filtering in treatment: 9528986 INFO @ Fri, 05 Jul 2019 10:48:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:48:10: #1 finished! INFO @ Fri, 05 Jul 2019 10:48:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:48:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:48:12: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:48:12: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:48:12: #1 total tags in treatment: 9529227 INFO @ Fri, 05 Jul 2019 10:48:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:48:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:48:12: #1 tags after filtering in treatment: 9528986 INFO @ Fri, 05 Jul 2019 10:48:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:48:12: #1 finished! INFO @ Fri, 05 Jul 2019 10:48:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:48:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:48:13: 9000000 INFO @ Fri, 05 Jul 2019 10:48:13: #2 number of paired peaks: 58549 INFO @ Fri, 05 Jul 2019 10:48:13: start model_add_line... INFO @ Fri, 05 Jul 2019 10:48:13: start X-correlation... INFO @ Fri, 05 Jul 2019 10:48:13: end of X-cor INFO @ Fri, 05 Jul 2019 10:48:13: #2 finished! INFO @ Fri, 05 Jul 2019 10:48:13: #2 predicted fragment length is 117 bps INFO @ Fri, 05 Jul 2019 10:48:13: #2 alternative fragment length(s) may be 117 bps INFO @ Fri, 05 Jul 2019 10:48:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.05_model.r INFO @ Fri, 05 Jul 2019 10:48:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:48:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:48:15: #2 number of paired peaks: 58549 INFO @ Fri, 05 Jul 2019 10:48:15: start model_add_line... INFO @ Fri, 05 Jul 2019 10:48:15: start X-correlation... INFO @ Fri, 05 Jul 2019 10:48:15: end of X-cor INFO @ Fri, 05 Jul 2019 10:48:15: #2 finished! INFO @ Fri, 05 Jul 2019 10:48:15: #2 predicted fragment length is 117 bps INFO @ Fri, 05 Jul 2019 10:48:15: #2 alternative fragment length(s) may be 117 bps INFO @ Fri, 05 Jul 2019 10:48:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.20_model.r INFO @ Fri, 05 Jul 2019 10:48:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:48:17: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:48:17: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:48:17: #1 total tags in treatment: 9529227 INFO @ Fri, 05 Jul 2019 10:48:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:48:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:48:17: #1 tags after filtering in treatment: 9528986 INFO @ Fri, 05 Jul 2019 10:48:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:48:17: #1 finished! INFO @ Fri, 05 Jul 2019 10:48:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:48:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:48:20: #2 number of paired peaks: 58549 INFO @ Fri, 05 Jul 2019 10:48:22: start model_add_line... INFO @ Fri, 05 Jul 2019 10:48:22: start X-correlation... INFO @ Fri, 05 Jul 2019 10:48:22: end of X-cor INFO @ Fri, 05 Jul 2019 10:48:22: #2 finished! INFO @ Fri, 05 Jul 2019 10:48:22: #2 predicted fragment length is 117 bps INFO @ Fri, 05 Jul 2019 10:48:22: #2 alternative fragment length(s) may be 117 bps INFO @ Fri, 05 Jul 2019 10:48:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.10_model.r INFO @ Fri, 05 Jul 2019 10:48:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:48:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:48:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:48:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:48:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:49:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:49:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:49:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.05_summits.bed INFO @ Fri, 05 Jul 2019 10:49:01: Done! INFO @ Fri, 05 Jul 2019 10:49:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.20_peaks.xls pass1 - making usageList (127 chroms): 15 millis INFO @ Fri, 05 Jul 2019 10:49:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.20_peaks.narrowPeak pass2 - checking and writing primary data (38313 records, 4 fields): 57 millis INFO @ Fri, 05 Jul 2019 10:49:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.20_summits.bed INFO @ Fri, 05 Jul 2019 10:49:02: Done! pass1 - making usageList (73 chroms): 3 millis pass2 - checking and writing primary data (13489 records, 4 fields): 21 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:49:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:49:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:49:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190364/ERX190364.10_summits.bed INFO @ Fri, 05 Jul 2019 10:49:10: Done! pass1 - making usageList (102 chroms): 5 millis pass2 - checking and writing primary data (24569 records, 4 fields): 35 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。