Job ID = 2002178 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 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: 00:04:22 15632543 reads; of these: 15632543 (100.00%) were unpaired; of these: 3188832 (20.40%) aligned 0 times 9726175 (62.22%) aligned exactly 1 time 2717536 (17.38%) aligned >1 times 79.60% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 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] 2914383 / 12443711 = 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 11:11:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.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 11:11:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:11:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:11:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.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 11:11:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:11:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:11:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.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 11:11:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:11:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:11:19: 1000000 INFO @ Fri, 05 Jul 2019 11:11:19: 1000000 INFO @ Fri, 05 Jul 2019 11:11:20: 1000000 INFO @ Fri, 05 Jul 2019 11:11:25: 2000000 INFO @ Fri, 05 Jul 2019 11:11:26: 2000000 INFO @ Fri, 05 Jul 2019 11:11:26: 2000000 INFO @ Fri, 05 Jul 2019 11:11:32: 3000000 INFO @ Fri, 05 Jul 2019 11:11:33: 3000000 INFO @ Fri, 05 Jul 2019 11:11:33: 3000000 INFO @ Fri, 05 Jul 2019 11:11:38: 4000000 INFO @ Fri, 05 Jul 2019 11:11:39: 4000000 INFO @ Fri, 05 Jul 2019 11:11:39: 4000000 INFO @ Fri, 05 Jul 2019 11:11:45: 5000000 INFO @ Fri, 05 Jul 2019 11:11:45: 5000000 INFO @ Fri, 05 Jul 2019 11:11:46: 5000000 INFO @ Fri, 05 Jul 2019 11:11:52: 6000000 INFO @ Fri, 05 Jul 2019 11:11:53: 6000000 INFO @ Fri, 05 Jul 2019 11:11:54: 6000000 INFO @ Fri, 05 Jul 2019 11:11:59: 7000000 INFO @ Fri, 05 Jul 2019 11:11:59: 7000000 INFO @ Fri, 05 Jul 2019 11:12:00: 7000000 INFO @ Fri, 05 Jul 2019 11:12:06: 8000000 INFO @ Fri, 05 Jul 2019 11:12:06: 8000000 INFO @ Fri, 05 Jul 2019 11:12:07: 8000000 INFO @ Fri, 05 Jul 2019 11:12:13: 9000000 INFO @ Fri, 05 Jul 2019 11:12:13: 9000000 INFO @ Fri, 05 Jul 2019 11:12:14: 9000000 INFO @ Fri, 05 Jul 2019 11:12:17: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:12:17: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:12:17: #1 total tags in treatment: 9529328 INFO @ Fri, 05 Jul 2019 11:12:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:12:17: #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 11:12:17: #1 tags after filtering in treatment: 9529105 INFO @ Fri, 05 Jul 2019 11:12:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:12:17: #1 finished! INFO @ Fri, 05 Jul 2019 11:12:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:12:17: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:12:17: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:12:17: #1 total tags in treatment: 9529328 INFO @ Fri, 05 Jul 2019 11:12:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:12:17: #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 11:12:17: #1 tags after filtering in treatment: 9529105 INFO @ Fri, 05 Jul 2019 11:12:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:12:17: #1 finished! INFO @ Fri, 05 Jul 2019 11:12:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:12:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:12:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:12:18: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:12:18: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:12:18: #1 total tags in treatment: 9529328 INFO @ Fri, 05 Jul 2019 11:12:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:12:18: #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 11:12:18: #1 tags after filtering in treatment: 9529105 INFO @ Fri, 05 Jul 2019 11:12:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:12:18: #1 finished! INFO @ Fri, 05 Jul 2019 11:12:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:12:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:12:21: #2 number of paired peaks: 58500 INFO @ Fri, 05 Jul 2019 11:12:21: start model_add_line... INFO @ Fri, 05 Jul 2019 11:12:21: #2 number of paired peaks: 58500 INFO @ Fri, 05 Jul 2019 11:12:21: start model_add_line... INFO @ Fri, 05 Jul 2019 11:12:21: #2 number of paired peaks: 58500 INFO @ Fri, 05 Jul 2019 11:12:21: start model_add_line... INFO @ Fri, 05 Jul 2019 11:12:21: start X-correlation... INFO @ Fri, 05 Jul 2019 11:12:21: end of X-cor INFO @ Fri, 05 Jul 2019 11:12:21: #2 finished! INFO @ Fri, 05 Jul 2019 11:12:21: start X-correlation... INFO @ Fri, 05 Jul 2019 11:12:21: end of X-cor INFO @ Fri, 05 Jul 2019 11:12:21: #2 finished! INFO @ Fri, 05 Jul 2019 11:12:21: #2 predicted fragment length is 117 bps INFO @ Fri, 05 Jul 2019 11:12:21: #2 predicted fragment length is 117 bps INFO @ Fri, 05 Jul 2019 11:12:21: #2 alternative fragment length(s) may be 117 bps INFO @ Fri, 05 Jul 2019 11:12:21: #2 alternative fragment length(s) may be 117 bps INFO @ Fri, 05 Jul 2019 11:12:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.20_model.r INFO @ Fri, 05 Jul 2019 11:12:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.05_model.r INFO @ Fri, 05 Jul 2019 11:12:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:12:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:12:21: start X-correlation... INFO @ Fri, 05 Jul 2019 11:12:21: end of X-cor INFO @ Fri, 05 Jul 2019 11:12:21: #2 finished! INFO @ Fri, 05 Jul 2019 11:12:21: #2 predicted fragment length is 117 bps INFO @ Fri, 05 Jul 2019 11:12:21: #2 alternative fragment length(s) may be 117 bps INFO @ Fri, 05 Jul 2019 11:12:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.10_model.r INFO @ Fri, 05 Jul 2019 11:12:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:12:51: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:12:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:12:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:13:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:13:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:13:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.10_summits.bed INFO @ Fri, 05 Jul 2019 11:13:08: Done! INFO @ Fri, 05 Jul 2019 11:13:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:13:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:13:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:13:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:13:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.05_summits.bed INFO @ Fri, 05 Jul 2019 11:13:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210258/ERX210258.20_summits.bed INFO @ Fri, 05 Jul 2019 11:13:09: Done! INFO @ Fri, 05 Jul 2019 11:13:09: Done! pass1 - making usageList (75 chroms): 7 millis pass2 - checking and writing primary data (13497 records, 4 fields): 25 millis pass1 - making usageList (128 chroms): 7 millis pass2 - checking and writing primary data (38334 records, 4 fields): 54 millis pass1 - making usageList (102 chroms): 8 millis pass2 - checking and writing primary data (24507 records, 4 fields): 35 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。