Job ID = 1294463 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,362,381 reads read : 14,362,381 reads written : 14,362,381 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:00 Multiseed full-index search: 00:04:07 14362381 reads; of these: 14362381 (100.00%) were unpaired; of these: 935714 (6.52%) aligned 0 times 12199232 (84.94%) aligned exactly 1 time 1227435 (8.55%) aligned >1 times 93.48% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1599275 / 13426667 = 0.1191 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 @ Mon, 03 Jun 2019 08:21:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 08:21:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:21:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:21:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 08:21:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:21:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:21:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 08:21:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:21:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:21:26: 1000000 INFO @ Mon, 03 Jun 2019 08:21:26: 1000000 INFO @ Mon, 03 Jun 2019 08:21:27: 1000000 INFO @ Mon, 03 Jun 2019 08:21:33: 2000000 INFO @ Mon, 03 Jun 2019 08:21:34: 2000000 INFO @ Mon, 03 Jun 2019 08:21:35: 2000000 INFO @ Mon, 03 Jun 2019 08:21:41: 3000000 INFO @ Mon, 03 Jun 2019 08:21:41: 3000000 INFO @ Mon, 03 Jun 2019 08:21:43: 3000000 INFO @ Mon, 03 Jun 2019 08:21:48: 4000000 INFO @ Mon, 03 Jun 2019 08:21:49: 4000000 INFO @ Mon, 03 Jun 2019 08:21:52: 4000000 INFO @ Mon, 03 Jun 2019 08:21:57: 5000000 INFO @ Mon, 03 Jun 2019 08:21:59: 5000000 INFO @ Mon, 03 Jun 2019 08:22:02: 5000000 INFO @ Mon, 03 Jun 2019 08:22:05: 6000000 INFO @ Mon, 03 Jun 2019 08:22:07: 6000000 INFO @ Mon, 03 Jun 2019 08:22:11: 6000000 INFO @ Mon, 03 Jun 2019 08:22:13: 7000000 INFO @ Mon, 03 Jun 2019 08:22:15: 7000000 INFO @ Mon, 03 Jun 2019 08:22:20: 7000000 INFO @ Mon, 03 Jun 2019 08:22:20: 8000000 INFO @ Mon, 03 Jun 2019 08:22:23: 8000000 INFO @ Mon, 03 Jun 2019 08:22:28: 9000000 INFO @ Mon, 03 Jun 2019 08:22:28: 8000000 INFO @ Mon, 03 Jun 2019 08:22:31: 9000000 INFO @ Mon, 03 Jun 2019 08:22:36: 10000000 INFO @ Mon, 03 Jun 2019 08:22:37: 9000000 INFO @ Mon, 03 Jun 2019 08:22:39: 10000000 INFO @ Mon, 03 Jun 2019 08:22:44: 11000000 INFO @ Mon, 03 Jun 2019 08:22:46: 10000000 INFO @ Mon, 03 Jun 2019 08:22:48: 11000000 INFO @ Mon, 03 Jun 2019 08:22:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:22:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:22:50: #1 total tags in treatment: 11827392 INFO @ Mon, 03 Jun 2019 08:22:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:22:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:22:51: #1 tags after filtering in treatment: 11827392 INFO @ Mon, 03 Jun 2019 08:22:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:22:51: #1 finished! INFO @ Mon, 03 Jun 2019 08:22:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:22:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:22:52: #2 number of paired peaks: 1372 INFO @ Mon, 03 Jun 2019 08:22:52: start model_add_line... INFO @ Mon, 03 Jun 2019 08:22:52: start X-correlation... INFO @ Mon, 03 Jun 2019 08:22:52: end of X-cor INFO @ Mon, 03 Jun 2019 08:22:52: #2 finished! INFO @ Mon, 03 Jun 2019 08:22:52: #2 predicted fragment length is 291 bps INFO @ Mon, 03 Jun 2019 08:22:52: #2 alternative fragment length(s) may be 3,291,293 bps INFO @ Mon, 03 Jun 2019 08:22:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.05_model.r INFO @ Mon, 03 Jun 2019 08:22:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:22:54: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:22:54: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:22:54: #1 total tags in treatment: 11827392 INFO @ Mon, 03 Jun 2019 08:22:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:22:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:22:55: #1 tags after filtering in treatment: 11827392 INFO @ Mon, 03 Jun 2019 08:22:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:22:55: #1 finished! INFO @ Mon, 03 Jun 2019 08:22:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:22:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:22:55: 11000000 INFO @ Mon, 03 Jun 2019 08:22:56: #2 number of paired peaks: 1372 INFO @ Mon, 03 Jun 2019 08:22:56: start model_add_line... INFO @ Mon, 03 Jun 2019 08:22:56: start X-correlation... INFO @ Mon, 03 Jun 2019 08:22:56: end of X-cor INFO @ Mon, 03 Jun 2019 08:22:56: #2 finished! INFO @ Mon, 03 Jun 2019 08:22:56: #2 predicted fragment length is 291 bps INFO @ Mon, 03 Jun 2019 08:22:56: #2 alternative fragment length(s) may be 3,291,293 bps INFO @ Mon, 03 Jun 2019 08:22:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.20_model.r INFO @ Mon, 03 Jun 2019 08:22:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:22:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:23:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:23:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:23:02: #1 total tags in treatment: 11827392 INFO @ Mon, 03 Jun 2019 08:23:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:23:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:23:02: #1 tags after filtering in treatment: 11827392 INFO @ Mon, 03 Jun 2019 08:23:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:23:02: #1 finished! INFO @ Mon, 03 Jun 2019 08:23:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:23:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:23:03: #2 number of paired peaks: 1372 INFO @ Mon, 03 Jun 2019 08:23:03: start model_add_line... INFO @ Mon, 03 Jun 2019 08:23:03: start X-correlation... INFO @ Mon, 03 Jun 2019 08:23:03: end of X-cor INFO @ Mon, 03 Jun 2019 08:23:03: #2 finished! INFO @ Mon, 03 Jun 2019 08:23:03: #2 predicted fragment length is 291 bps INFO @ Mon, 03 Jun 2019 08:23:03: #2 alternative fragment length(s) may be 3,291,293 bps INFO @ Mon, 03 Jun 2019 08:23:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.10_model.r INFO @ Mon, 03 Jun 2019 08:23:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:23:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:23:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:23:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:23:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:23:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:23:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:23:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.05_summits.bed INFO @ Mon, 03 Jun 2019 08:23:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3678 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:23:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:23:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:23:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.20_summits.bed INFO @ Mon, 03 Jun 2019 08:23:53: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (551 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:24:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:24:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:24:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287664/SRX287664.10_summits.bed INFO @ Mon, 03 Jun 2019 08:24:01: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1749 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。