Job ID = 2001698 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,203,213 reads read : 19,203,213 reads written : 19,203,213 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: 00:00:01 Multiseed full-index search: 00:04:06 19203213 reads; of these: 19203213 (100.00%) were unpaired; of these: 493219 (2.57%) aligned 0 times 16917467 (88.10%) aligned exactly 1 time 1792527 (9.33%) aligned >1 times 97.43% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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] 9783182 / 18709994 = 0.5229 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 09:09:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.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 09:09:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:09:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:09:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.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 09:09:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:09:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.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 09:09:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:09:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:10:02: 1000000 INFO @ Fri, 05 Jul 2019 09:10:05: 1000000 INFO @ Fri, 05 Jul 2019 09:10:06: 1000000 INFO @ Fri, 05 Jul 2019 09:10:09: 2000000 INFO @ Fri, 05 Jul 2019 09:10:13: 2000000 INFO @ Fri, 05 Jul 2019 09:10:16: 2000000 INFO @ Fri, 05 Jul 2019 09:10:17: 3000000 INFO @ Fri, 05 Jul 2019 09:10:22: 3000000 INFO @ Fri, 05 Jul 2019 09:10:24: 4000000 INFO @ Fri, 05 Jul 2019 09:10:26: 3000000 INFO @ Fri, 05 Jul 2019 09:10:30: 4000000 INFO @ Fri, 05 Jul 2019 09:10:31: 5000000 INFO @ Fri, 05 Jul 2019 09:10:35: 4000000 INFO @ Fri, 05 Jul 2019 09:10:38: 6000000 INFO @ Fri, 05 Jul 2019 09:10:39: 5000000 INFO @ Fri, 05 Jul 2019 09:10:45: 5000000 INFO @ Fri, 05 Jul 2019 09:10:45: 7000000 INFO @ Fri, 05 Jul 2019 09:10:47: 6000000 INFO @ Fri, 05 Jul 2019 09:10:53: 8000000 INFO @ Fri, 05 Jul 2019 09:10:54: 6000000 INFO @ Fri, 05 Jul 2019 09:10:55: 7000000 INFO @ Fri, 05 Jul 2019 09:10:59: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:10:59: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:10:59: #1 total tags in treatment: 8926812 INFO @ Fri, 05 Jul 2019 09:10:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:10:59: #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 09:10:59: #1 tags after filtering in treatment: 8926559 INFO @ Fri, 05 Jul 2019 09:10:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:10:59: #1 finished! INFO @ Fri, 05 Jul 2019 09:10:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:10:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:11:02: #2 number of paired peaks: 41818 INFO @ Fri, 05 Jul 2019 09:11:02: start model_add_line... INFO @ Fri, 05 Jul 2019 09:11:02: start X-correlation... INFO @ Fri, 05 Jul 2019 09:11:02: end of X-cor INFO @ Fri, 05 Jul 2019 09:11:02: #2 finished! INFO @ Fri, 05 Jul 2019 09:11:02: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 09:11:02: #2 alternative fragment length(s) may be 136,475 bps INFO @ Fri, 05 Jul 2019 09:11:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.05_model.r INFO @ Fri, 05 Jul 2019 09:11:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:11:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:11:03: 7000000 INFO @ Fri, 05 Jul 2019 09:11:04: 8000000 INFO @ Fri, 05 Jul 2019 09:11:11: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:11:11: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:11:11: #1 total tags in treatment: 8926812 INFO @ Fri, 05 Jul 2019 09:11:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:11:11: #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 09:11:12: #1 tags after filtering in treatment: 8926559 INFO @ Fri, 05 Jul 2019 09:11:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:11:12: #1 finished! INFO @ Fri, 05 Jul 2019 09:11:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:11:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:11:12: 8000000 INFO @ Fri, 05 Jul 2019 09:11:14: #2 number of paired peaks: 41818 INFO @ Fri, 05 Jul 2019 09:11:14: start model_add_line... INFO @ Fri, 05 Jul 2019 09:11:14: start X-correlation... INFO @ Fri, 05 Jul 2019 09:11:14: end of X-cor INFO @ Fri, 05 Jul 2019 09:11:14: #2 finished! INFO @ Fri, 05 Jul 2019 09:11:14: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 09:11:14: #2 alternative fragment length(s) may be 136,475 bps INFO @ Fri, 05 Jul 2019 09:11:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.10_model.r INFO @ Fri, 05 Jul 2019 09:11:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:11:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:11:21: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:11:21: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:11:21: #1 total tags in treatment: 8926812 INFO @ Fri, 05 Jul 2019 09:11:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:11:21: #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 09:11:21: #1 tags after filtering in treatment: 8926559 INFO @ Fri, 05 Jul 2019 09:11:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:11:21: #1 finished! INFO @ Fri, 05 Jul 2019 09:11:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:11:23: #2 number of paired peaks: 41818 INFO @ Fri, 05 Jul 2019 09:11:23: start model_add_line... INFO @ Fri, 05 Jul 2019 09:11:24: start X-correlation... INFO @ Fri, 05 Jul 2019 09:11:24: end of X-cor INFO @ Fri, 05 Jul 2019 09:11:24: #2 finished! INFO @ Fri, 05 Jul 2019 09:11:24: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 09:11:24: #2 alternative fragment length(s) may be 136,475 bps INFO @ Fri, 05 Jul 2019 09:11:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.20_model.r INFO @ Fri, 05 Jul 2019 09:11:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:11:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:11:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:11:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:11:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:11:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:11:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.05_summits.bed INFO @ Fri, 05 Jul 2019 09:11:46: Done! pass1 - making usageList (125 chroms): 15 millis pass2 - checking and writing primary data (40962 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:11:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:11:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:11:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:11:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.10_summits.bed INFO @ Fri, 05 Jul 2019 09:11:56: Done! pass1 - making usageList (106 chroms): 6 millis pass2 - checking and writing primary data (32057 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:12:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:12:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102008/ERX102008.20_summits.bed INFO @ Fri, 05 Jul 2019 09:12:08: Done! pass1 - making usageList (82 chroms): 5 millis pass2 - checking and writing primary data (20943 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。