Job ID = 1293285 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,125,196 reads read : 27,125,196 reads written : 27,125,196 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: 00:08:31 27125196 reads; of these: 27125196 (100.00%) were unpaired; of these: 1045561 (3.85%) aligned 0 times 20213801 (74.52%) aligned exactly 1 time 5865834 (21.63%) aligned >1 times 96.15% overall alignment rate Time searching: 00:08:31 Overall time: 00:08:31 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] 12209259 / 26079635 = 0.4682 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 @ Sun, 02 Jun 2019 23:01:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.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 @ Sun, 02 Jun 2019 23:01:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:01:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:01:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.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 @ Sun, 02 Jun 2019 23:01:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:01:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.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 @ Sun, 02 Jun 2019 23:01:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:01:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:01:22: 1000000 INFO @ Sun, 02 Jun 2019 23:01:23: 1000000 INFO @ Sun, 02 Jun 2019 23:01:24: 1000000 INFO @ Sun, 02 Jun 2019 23:01:31: 2000000 INFO @ Sun, 02 Jun 2019 23:01:32: 2000000 INFO @ Sun, 02 Jun 2019 23:01:36: 2000000 INFO @ Sun, 02 Jun 2019 23:01:41: 3000000 INFO @ Sun, 02 Jun 2019 23:01:42: 3000000 INFO @ Sun, 02 Jun 2019 23:01:47: 3000000 INFO @ Sun, 02 Jun 2019 23:01:50: 4000000 INFO @ Sun, 02 Jun 2019 23:01:51: 4000000 INFO @ Sun, 02 Jun 2019 23:01:58: 4000000 INFO @ Sun, 02 Jun 2019 23:01:59: 5000000 INFO @ Sun, 02 Jun 2019 23:02:01: 5000000 INFO @ Sun, 02 Jun 2019 23:02:08: 6000000 INFO @ Sun, 02 Jun 2019 23:02:10: 6000000 INFO @ Sun, 02 Jun 2019 23:02:11: 5000000 INFO @ Sun, 02 Jun 2019 23:02:17: 7000000 INFO @ Sun, 02 Jun 2019 23:02:19: 7000000 INFO @ Sun, 02 Jun 2019 23:02:23: 6000000 INFO @ Sun, 02 Jun 2019 23:02:26: 8000000 INFO @ Sun, 02 Jun 2019 23:02:29: 8000000 INFO @ Sun, 02 Jun 2019 23:02:35: 7000000 INFO @ Sun, 02 Jun 2019 23:02:35: 9000000 INFO @ Sun, 02 Jun 2019 23:02:39: 9000000 INFO @ Sun, 02 Jun 2019 23:02:44: 10000000 INFO @ Sun, 02 Jun 2019 23:02:47: 8000000 INFO @ Sun, 02 Jun 2019 23:02:48: 10000000 INFO @ Sun, 02 Jun 2019 23:02:54: 11000000 INFO @ Sun, 02 Jun 2019 23:02:58: 11000000 INFO @ Sun, 02 Jun 2019 23:02:59: 9000000 INFO @ Sun, 02 Jun 2019 23:03:04: 12000000 INFO @ Sun, 02 Jun 2019 23:03:08: 12000000 INFO @ Sun, 02 Jun 2019 23:03:11: 10000000 INFO @ Sun, 02 Jun 2019 23:03:14: 13000000 INFO @ Sun, 02 Jun 2019 23:03:18: 13000000 INFO @ Sun, 02 Jun 2019 23:03:22: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:03:22: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:03:22: #1 total tags in treatment: 13870376 INFO @ Sun, 02 Jun 2019 23:03:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:03:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:03:22: #1 tags after filtering in treatment: 13870376 INFO @ Sun, 02 Jun 2019 23:03:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:03:22: #1 finished! INFO @ Sun, 02 Jun 2019 23:03:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:03:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:03:24: 11000000 INFO @ Sun, 02 Jun 2019 23:03:24: #2 number of paired peaks: 3224 INFO @ Sun, 02 Jun 2019 23:03:24: start model_add_line... INFO @ Sun, 02 Jun 2019 23:03:24: start X-correlation... INFO @ Sun, 02 Jun 2019 23:03:24: end of X-cor INFO @ Sun, 02 Jun 2019 23:03:24: #2 finished! INFO @ Sun, 02 Jun 2019 23:03:24: #2 predicted fragment length is 188 bps INFO @ Sun, 02 Jun 2019 23:03:24: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 02 Jun 2019 23:03:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.05_model.r INFO @ Sun, 02 Jun 2019 23:03:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:03:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:03:25: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:03:25: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:03:25: #1 total tags in treatment: 13870376 INFO @ Sun, 02 Jun 2019 23:03:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:03:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:03:26: #1 tags after filtering in treatment: 13870376 INFO @ Sun, 02 Jun 2019 23:03:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:03:26: #1 finished! INFO @ Sun, 02 Jun 2019 23:03:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:03:27: #2 number of paired peaks: 3224 INFO @ Sun, 02 Jun 2019 23:03:27: start model_add_line... INFO @ Sun, 02 Jun 2019 23:03:28: start X-correlation... INFO @ Sun, 02 Jun 2019 23:03:28: end of X-cor INFO @ Sun, 02 Jun 2019 23:03:28: #2 finished! INFO @ Sun, 02 Jun 2019 23:03:28: #2 predicted fragment length is 188 bps INFO @ Sun, 02 Jun 2019 23:03:28: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 02 Jun 2019 23:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.20_model.r INFO @ Sun, 02 Jun 2019 23:03:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:03:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:03:35: 12000000 INFO @ Sun, 02 Jun 2019 23:03:46: 13000000 INFO @ Sun, 02 Jun 2019 23:03:56: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:03:56: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:03:56: #1 total tags in treatment: 13870376 INFO @ Sun, 02 Jun 2019 23:03:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:03:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:03:56: #1 tags after filtering in treatment: 13870376 INFO @ Sun, 02 Jun 2019 23:03:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:03:56: #1 finished! INFO @ Sun, 02 Jun 2019 23:03:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:03:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:03:58: #2 number of paired peaks: 3224 INFO @ Sun, 02 Jun 2019 23:03:58: start model_add_line... INFO @ Sun, 02 Jun 2019 23:03:58: start X-correlation... INFO @ Sun, 02 Jun 2019 23:03:58: end of X-cor INFO @ Sun, 02 Jun 2019 23:03:58: #2 finished! INFO @ Sun, 02 Jun 2019 23:03:58: #2 predicted fragment length is 188 bps INFO @ Sun, 02 Jun 2019 23:03:58: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 02 Jun 2019 23:03:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.10_model.r INFO @ Sun, 02 Jun 2019 23:03:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:03:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:04:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:04:15: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:04:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:04:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:04:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.05_summits.bed INFO @ Sun, 02 Jun 2019 23:04:32: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8774 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:04:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:04:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:04:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.20_summits.bed INFO @ Sun, 02 Jun 2019 23:04:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5002 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:04:45: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 23:05:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:05:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:05:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011421/ERX011421.10_summits.bed INFO @ Sun, 02 Jun 2019 23:05:05: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6914 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。