Job ID = 2002531 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,270,222 reads read : 22,270,222 reads written : 22,270,222 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR572172.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:21:57 22270222 reads; of these: 22270222 (100.00%) were unpaired; of these: 2809348 (12.61%) aligned 0 times 16905518 (75.91%) aligned exactly 1 time 2555356 (11.47%) aligned >1 times 87.39% overall alignment rate Time searching: 00:21:58 Overall time: 00:21:58 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] 4997354 / 19460874 = 0.2568 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 12:22:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.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 12:22:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:22:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.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 12:22:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:22:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:22:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.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 12:22:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:22:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:22:38: 1000000 INFO @ Fri, 05 Jul 2019 12:22:40: 1000000 INFO @ Fri, 05 Jul 2019 12:22:43: 1000000 INFO @ Fri, 05 Jul 2019 12:22:49: 2000000 INFO @ Fri, 05 Jul 2019 12:22:55: 2000000 INFO @ Fri, 05 Jul 2019 12:22:58: 2000000 INFO @ Fri, 05 Jul 2019 12:23:01: 3000000 INFO @ Fri, 05 Jul 2019 12:23:10: 3000000 INFO @ Fri, 05 Jul 2019 12:23:12: 4000000 INFO @ Fri, 05 Jul 2019 12:23:14: 3000000 INFO @ Fri, 05 Jul 2019 12:23:24: 5000000 INFO @ Fri, 05 Jul 2019 12:23:24: 4000000 INFO @ Fri, 05 Jul 2019 12:23:28: 4000000 INFO @ Fri, 05 Jul 2019 12:23:35: 6000000 INFO @ Fri, 05 Jul 2019 12:23:39: 5000000 INFO @ Fri, 05 Jul 2019 12:23:43: 5000000 INFO @ Fri, 05 Jul 2019 12:23:46: 7000000 INFO @ Fri, 05 Jul 2019 12:23:53: 6000000 INFO @ Fri, 05 Jul 2019 12:23:58: 8000000 INFO @ Fri, 05 Jul 2019 12:23:58: 6000000 INFO @ Fri, 05 Jul 2019 12:24:06: 7000000 INFO @ Fri, 05 Jul 2019 12:24:09: 9000000 INFO @ Fri, 05 Jul 2019 12:24:12: 7000000 INFO @ Fri, 05 Jul 2019 12:24:20: 10000000 INFO @ Fri, 05 Jul 2019 12:24:20: 8000000 INFO @ Fri, 05 Jul 2019 12:24:27: 8000000 INFO @ Fri, 05 Jul 2019 12:24:32: 11000000 INFO @ Fri, 05 Jul 2019 12:24:34: 9000000 INFO @ Fri, 05 Jul 2019 12:24:41: 9000000 INFO @ Fri, 05 Jul 2019 12:24:43: 12000000 INFO @ Fri, 05 Jul 2019 12:24:48: 10000000 INFO @ Fri, 05 Jul 2019 12:24:55: 13000000 INFO @ Fri, 05 Jul 2019 12:24:56: 10000000 INFO @ Fri, 05 Jul 2019 12:25:03: 11000000 INFO @ Fri, 05 Jul 2019 12:25:07: 14000000 INFO @ Fri, 05 Jul 2019 12:25:11: 11000000 INFO @ Fri, 05 Jul 2019 12:25:13: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 12:25:13: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 12:25:13: #1 total tags in treatment: 14463520 INFO @ Fri, 05 Jul 2019 12:25:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:25:13: #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 12:25:13: #1 tags after filtering in treatment: 14463235 INFO @ Fri, 05 Jul 2019 12:25:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:25:13: #1 finished! INFO @ Fri, 05 Jul 2019 12:25:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:25:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:25:16: #2 number of paired peaks: 24712 INFO @ Fri, 05 Jul 2019 12:25:16: start model_add_line... INFO @ Fri, 05 Jul 2019 12:25:16: start X-correlation... INFO @ Fri, 05 Jul 2019 12:25:16: end of X-cor INFO @ Fri, 05 Jul 2019 12:25:16: #2 finished! INFO @ Fri, 05 Jul 2019 12:25:16: #2 predicted fragment length is 245 bps INFO @ Fri, 05 Jul 2019 12:25:16: #2 alternative fragment length(s) may be 245 bps INFO @ Fri, 05 Jul 2019 12:25:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.10_model.r INFO @ Fri, 05 Jul 2019 12:25:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:25:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:25:17: 12000000 INFO @ Fri, 05 Jul 2019 12:25:26: 12000000 INFO @ Fri, 05 Jul 2019 12:25:31: 13000000 INFO @ Fri, 05 Jul 2019 12:25:41: 13000000 INFO @ Fri, 05 Jul 2019 12:25:45: 14000000 INFO @ Fri, 05 Jul 2019 12:25:52: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 12:25:52: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 12:25:52: #1 total tags in treatment: 14463520 INFO @ Fri, 05 Jul 2019 12:25:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:25:52: #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 12:25:52: #1 tags after filtering in treatment: 14463235 INFO @ Fri, 05 Jul 2019 12:25:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:25:52: #1 finished! INFO @ Fri, 05 Jul 2019 12:25:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:25:55: #2 number of paired peaks: 24712 INFO @ Fri, 05 Jul 2019 12:25:55: start model_add_line... INFO @ Fri, 05 Jul 2019 12:25:55: start X-correlation... INFO @ Fri, 05 Jul 2019 12:25:55: end of X-cor INFO @ Fri, 05 Jul 2019 12:25:55: #2 finished! INFO @ Fri, 05 Jul 2019 12:25:55: #2 predicted fragment length is 245 bps INFO @ Fri, 05 Jul 2019 12:25:55: #2 alternative fragment length(s) may be 245 bps INFO @ Fri, 05 Jul 2019 12:25:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.05_model.r INFO @ Fri, 05 Jul 2019 12:25:56: 14000000 INFO @ Fri, 05 Jul 2019 12:26:02: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 12:26:02: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 12:26:02: #1 total tags in treatment: 14463520 INFO @ Fri, 05 Jul 2019 12:26:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:26:02: #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 12:26:03: #1 tags after filtering in treatment: 14463235 INFO @ Fri, 05 Jul 2019 12:26:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:26:03: #1 finished! INFO @ Fri, 05 Jul 2019 12:26:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:26:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:26:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:26:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:26:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:26:05: #2 number of paired peaks: 24712 INFO @ Fri, 05 Jul 2019 12:26:05: start model_add_line... INFO @ Fri, 05 Jul 2019 12:26:05: start X-correlation... INFO @ Fri, 05 Jul 2019 12:26:05: end of X-cor INFO @ Fri, 05 Jul 2019 12:26:05: #2 finished! INFO @ Fri, 05 Jul 2019 12:26:05: #2 predicted fragment length is 245 bps INFO @ Fri, 05 Jul 2019 12:26:05: #2 alternative fragment length(s) may be 245 bps INFO @ Fri, 05 Jul 2019 12:26:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.20_model.r INFO @ Fri, 05 Jul 2019 12:26:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:26:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:26:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:26:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:26:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.10_summits.bed INFO @ Fri, 05 Jul 2019 12:26:28: Done! pass1 - making usageList (110 chroms): 3 millis pass2 - checking and writing primary data (16742 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:26:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:26:55: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:27:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:27:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:27:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.05_summits.bed INFO @ Fri, 05 Jul 2019 12:27:16: Done! pass1 - making usageList (128 chroms): 4 millis pass2 - checking and writing primary data (18553 records, 4 fields): 31 millis INFO @ Fri, 05 Jul 2019 12:27:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:27:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:27:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530959/ERX530959.20_summits.bed INFO @ Fri, 05 Jul 2019 12:27:18: Done! pass1 - making usageList (89 chroms): 4 millis pass2 - checking and writing primary data (14481 records, 4 fields): 24 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。