Job ID = 1293275 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T13:37:47 fasterq-dump.2.9.6 int: no error - skipping the cache-tee completely spots read : 41,247,126 reads read : 41,247,126 reads written : 41,247,126 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: 00:09:43 41247126 reads; of these: 41247126 (100.00%) were unpaired; of these: 7483446 (18.14%) aligned 0 times 27799976 (67.40%) aligned exactly 1 time 5963704 (14.46%) aligned >1 times 81.86% overall alignment rate Time searching: 00:09:43 Overall time: 00:09:44 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 12 files... [bam_rmdupse_core] 27216600 / 33763680 = 0.8061 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 23:08:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.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 23:08:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:08:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:08:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.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 23:08:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:08:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:08:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.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 23:08:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:08:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:08:24: 1000000 INFO @ Sun, 02 Jun 2019 23:08:26: 1000000 INFO @ Sun, 02 Jun 2019 23:08:26: 1000000 INFO @ Sun, 02 Jun 2019 23:08:33: 2000000 INFO @ Sun, 02 Jun 2019 23:08:36: 2000000 INFO @ Sun, 02 Jun 2019 23:08:36: 2000000 INFO @ Sun, 02 Jun 2019 23:08:42: 3000000 INFO @ Sun, 02 Jun 2019 23:08:46: 3000000 INFO @ Sun, 02 Jun 2019 23:08:47: 3000000 INFO @ Sun, 02 Jun 2019 23:08:52: 4000000 INFO @ Sun, 02 Jun 2019 23:08:57: 4000000 INFO @ Sun, 02 Jun 2019 23:08:57: 4000000 INFO @ Sun, 02 Jun 2019 23:09:01: 5000000 INFO @ Sun, 02 Jun 2019 23:09:08: 5000000 INFO @ Sun, 02 Jun 2019 23:09:09: 5000000 INFO @ Sun, 02 Jun 2019 23:09:10: 6000000 INFO @ Sun, 02 Jun 2019 23:09:14: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:09:14: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:09:14: #1 total tags in treatment: 6547080 INFO @ Sun, 02 Jun 2019 23:09:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:09:14: #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 23:09:14: #1 tags after filtering in treatment: 6547080 INFO @ Sun, 02 Jun 2019 23:09:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:09:14: #1 finished! INFO @ Sun, 02 Jun 2019 23:09:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:09:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:09:15: #2 number of paired peaks: 2330 INFO @ Sun, 02 Jun 2019 23:09:15: start model_add_line... INFO @ Sun, 02 Jun 2019 23:09:16: start X-correlation... INFO @ Sun, 02 Jun 2019 23:09:16: end of X-cor INFO @ Sun, 02 Jun 2019 23:09:16: #2 finished! INFO @ Sun, 02 Jun 2019 23:09:16: #2 predicted fragment length is 81 bps INFO @ Sun, 02 Jun 2019 23:09:16: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 02 Jun 2019 23:09:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.20_model.r INFO @ Sun, 02 Jun 2019 23:09:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:09:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:09:18: 6000000 INFO @ Sun, 02 Jun 2019 23:09:19: 6000000 INFO @ Sun, 02 Jun 2019 23:09:23: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:09:23: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:09:23: #1 total tags in treatment: 6547080 INFO @ Sun, 02 Jun 2019 23:09:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:09:23: #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 23:09:24: #1 tags after filtering in treatment: 6547080 INFO @ Sun, 02 Jun 2019 23:09:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:09:24: #1 finished! INFO @ Sun, 02 Jun 2019 23:09:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:09:24: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:09:24: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:09:24: #1 total tags in treatment: 6547080 INFO @ Sun, 02 Jun 2019 23:09:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:09:24: #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 23:09:24: #1 tags after filtering in treatment: 6547080 INFO @ Sun, 02 Jun 2019 23:09:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:09:24: #1 finished! INFO @ Sun, 02 Jun 2019 23:09:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:09:25: #2 number of paired peaks: 2330 INFO @ Sun, 02 Jun 2019 23:09:25: start model_add_line... INFO @ Sun, 02 Jun 2019 23:09:25: start X-correlation... INFO @ Sun, 02 Jun 2019 23:09:25: end of X-cor INFO @ Sun, 02 Jun 2019 23:09:25: #2 finished! INFO @ Sun, 02 Jun 2019 23:09:25: #2 predicted fragment length is 81 bps INFO @ Sun, 02 Jun 2019 23:09:25: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 02 Jun 2019 23:09:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.05_model.r INFO @ Sun, 02 Jun 2019 23:09:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:09:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:09:25: #2 number of paired peaks: 2330 INFO @ Sun, 02 Jun 2019 23:09:25: start model_add_line... INFO @ Sun, 02 Jun 2019 23:09:26: start X-correlation... INFO @ Sun, 02 Jun 2019 23:09:26: end of X-cor INFO @ Sun, 02 Jun 2019 23:09:26: #2 finished! INFO @ Sun, 02 Jun 2019 23:09:26: #2 predicted fragment length is 81 bps INFO @ Sun, 02 Jun 2019 23:09:26: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 02 Jun 2019 23:09:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.10_model.r INFO @ Sun, 02 Jun 2019 23:09:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:09:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:09:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:09:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:09:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:09:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:09:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:09:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.20_summits.bed INFO @ Sun, 02 Jun 2019 23:09:52: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2779 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:09:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:09:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:09:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.05_summits.bed INFO @ Sun, 02 Jun 2019 23:09:58: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (15012 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:09:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:09:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:09:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011414/ERX011414.10_summits.bed INFO @ Sun, 02 Jun 2019 23:09:59: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7218 records, 4 fields): 31 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。