Job ID = 2001154 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,105,295 reads read : 24,105,295 reads written : 24,105,295 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:08:25 24105295 reads; of these: 24105295 (100.00%) were unpaired; of these: 598698 (2.48%) aligned 0 times 18016818 (74.74%) aligned exactly 1 time 5489779 (22.77%) aligned >1 times 97.52% overall alignment rate Time searching: 00:08:26 Overall time: 00:08:26 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] 1558320 / 23506597 = 0.0663 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 04:09:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.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 04:09:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:09:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:09:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.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 04:09:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:09:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:09:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.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 04:09:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:09:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:09:52: 1000000 INFO @ Fri, 05 Jul 2019 04:09:54: 1000000 INFO @ Fri, 05 Jul 2019 04:09:54: 1000000 INFO @ Fri, 05 Jul 2019 04:10:02: 2000000 INFO @ Fri, 05 Jul 2019 04:10:02: 2000000 INFO @ Fri, 05 Jul 2019 04:10:03: 2000000 INFO @ Fri, 05 Jul 2019 04:10:11: 3000000 INFO @ Fri, 05 Jul 2019 04:10:11: 3000000 INFO @ Fri, 05 Jul 2019 04:10:13: 3000000 INFO @ Fri, 05 Jul 2019 04:10:19: 4000000 INFO @ Fri, 05 Jul 2019 04:10:21: 4000000 INFO @ Fri, 05 Jul 2019 04:10:23: 4000000 INFO @ Fri, 05 Jul 2019 04:10:27: 5000000 INFO @ Fri, 05 Jul 2019 04:10:30: 5000000 INFO @ Fri, 05 Jul 2019 04:10:33: 5000000 INFO @ Fri, 05 Jul 2019 04:10:36: 6000000 INFO @ Fri, 05 Jul 2019 04:10:40: 6000000 INFO @ Fri, 05 Jul 2019 04:10:42: 6000000 INFO @ Fri, 05 Jul 2019 04:10:44: 7000000 INFO @ Fri, 05 Jul 2019 04:10:50: 7000000 INFO @ Fri, 05 Jul 2019 04:10:52: 7000000 INFO @ Fri, 05 Jul 2019 04:10:53: 8000000 INFO @ Fri, 05 Jul 2019 04:10:59: 8000000 INFO @ Fri, 05 Jul 2019 04:11:01: 9000000 INFO @ Fri, 05 Jul 2019 04:11:02: 8000000 INFO @ Fri, 05 Jul 2019 04:11:09: 9000000 INFO @ Fri, 05 Jul 2019 04:11:10: 10000000 INFO @ Fri, 05 Jul 2019 04:11:12: 9000000 INFO @ Fri, 05 Jul 2019 04:11:18: 11000000 INFO @ Fri, 05 Jul 2019 04:11:18: 10000000 INFO @ Fri, 05 Jul 2019 04:11:21: 10000000 INFO @ Fri, 05 Jul 2019 04:11:26: 12000000 INFO @ Fri, 05 Jul 2019 04:11:28: 11000000 INFO @ Fri, 05 Jul 2019 04:11:31: 11000000 INFO @ Fri, 05 Jul 2019 04:11:35: 13000000 INFO @ Fri, 05 Jul 2019 04:11:38: 12000000 INFO @ Fri, 05 Jul 2019 04:11:41: 12000000 INFO @ Fri, 05 Jul 2019 04:11:43: 14000000 INFO @ Fri, 05 Jul 2019 04:11:47: 13000000 INFO @ Fri, 05 Jul 2019 04:11:51: 13000000 INFO @ Fri, 05 Jul 2019 04:11:52: 15000000 INFO @ Fri, 05 Jul 2019 04:11:57: 14000000 INFO @ Fri, 05 Jul 2019 04:12:00: 16000000 INFO @ Fri, 05 Jul 2019 04:12:01: 14000000 INFO @ Fri, 05 Jul 2019 04:12:06: 15000000 INFO @ Fri, 05 Jul 2019 04:12:09: 17000000 INFO @ Fri, 05 Jul 2019 04:12:10: 15000000 INFO @ Fri, 05 Jul 2019 04:12:15: 16000000 INFO @ Fri, 05 Jul 2019 04:12:17: 18000000 INFO @ Fri, 05 Jul 2019 04:12:20: 16000000 INFO @ Fri, 05 Jul 2019 04:12:24: 17000000 INFO @ Fri, 05 Jul 2019 04:12:25: 19000000 INFO @ Fri, 05 Jul 2019 04:12:29: 17000000 INFO @ Fri, 05 Jul 2019 04:12:34: 18000000 INFO @ Fri, 05 Jul 2019 04:12:34: 20000000 INFO @ Fri, 05 Jul 2019 04:12:39: 18000000 INFO @ Fri, 05 Jul 2019 04:12:42: 21000000 INFO @ Fri, 05 Jul 2019 04:12:44: 19000000 INFO @ Fri, 05 Jul 2019 04:12:48: 19000000 INFO @ Fri, 05 Jul 2019 04:12:50: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:12:50: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:12:50: #1 total tags in treatment: 21948277 INFO @ Fri, 05 Jul 2019 04:12:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:12:50: #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 04:12:51: #1 tags after filtering in treatment: 21948095 INFO @ Fri, 05 Jul 2019 04:12:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:12:51: #1 finished! INFO @ Fri, 05 Jul 2019 04:12:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:12:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:12:53: 20000000 INFO @ Fri, 05 Jul 2019 04:12:56: #2 number of paired peaks: 73880 INFO @ Fri, 05 Jul 2019 04:12:56: start model_add_line... INFO @ Fri, 05 Jul 2019 04:12:56: start X-correlation... INFO @ Fri, 05 Jul 2019 04:12:57: end of X-cor INFO @ Fri, 05 Jul 2019 04:12:57: #2 finished! INFO @ Fri, 05 Jul 2019 04:12:57: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 04:12:57: #2 alternative fragment length(s) may be 0,140,299,514 bps INFO @ Fri, 05 Jul 2019 04:12:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.20_model.r INFO @ Fri, 05 Jul 2019 04:12:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:12:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:12:58: 20000000 INFO @ Fri, 05 Jul 2019 04:13:03: 21000000 INFO @ Fri, 05 Jul 2019 04:13:07: 21000000 INFO @ Fri, 05 Jul 2019 04:13:12: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:13:12: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:13:12: #1 total tags in treatment: 21948277 INFO @ Fri, 05 Jul 2019 04:13:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:13:12: #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 04:13:12: #1 tags after filtering in treatment: 21948095 INFO @ Fri, 05 Jul 2019 04:13:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:13:12: #1 finished! INFO @ Fri, 05 Jul 2019 04:13:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:13:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:13:16: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:13:16: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:13:16: #1 total tags in treatment: 21948277 INFO @ Fri, 05 Jul 2019 04:13:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:13:16: #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 04:13:17: #1 tags after filtering in treatment: 21948095 INFO @ Fri, 05 Jul 2019 04:13:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:13:17: #1 finished! INFO @ Fri, 05 Jul 2019 04:13:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:13:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:13:18: #2 number of paired peaks: 73880 INFO @ Fri, 05 Jul 2019 04:13:18: start model_add_line... INFO @ Fri, 05 Jul 2019 04:13:18: start X-correlation... INFO @ Fri, 05 Jul 2019 04:13:18: end of X-cor INFO @ Fri, 05 Jul 2019 04:13:18: #2 finished! INFO @ Fri, 05 Jul 2019 04:13:18: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 04:13:18: #2 alternative fragment length(s) may be 0,140,299,514 bps INFO @ Fri, 05 Jul 2019 04:13:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.05_model.r INFO @ Fri, 05 Jul 2019 04:13:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:13:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:13:22: #2 number of paired peaks: 73880 INFO @ Fri, 05 Jul 2019 04:13:22: start model_add_line... INFO @ Fri, 05 Jul 2019 04:13:22: start X-correlation... INFO @ Fri, 05 Jul 2019 04:13:22: end of X-cor INFO @ Fri, 05 Jul 2019 04:13:22: #2 finished! INFO @ Fri, 05 Jul 2019 04:13:22: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 04:13:22: #2 alternative fragment length(s) may be 0,140,299,514 bps INFO @ Fri, 05 Jul 2019 04:13:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.10_model.r INFO @ Fri, 05 Jul 2019 04:13:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:13:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:14:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:14:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:14:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:14:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:14:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:14:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.20_summits.bed INFO @ Fri, 05 Jul 2019 04:14:46: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:15:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:15:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:15:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.05_summits.bed INFO @ Fri, 05 Jul 2019 04:15:07: Done! pass1 - making usageList (69 chroms): 1 millis pass2 - checking and writing primary data (4539 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:15:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:15:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:15:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101844/ERX101844.10_summits.bed INFO @ Fri, 05 Jul 2019 04:15:12: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (939 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。