Job ID = 1294113 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,538,591 reads read : 18,538,591 reads written : 18,538,591 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: 00:00:01 Multiseed full-index search: 00:07:33 18538591 reads; of these: 18538591 (100.00%) were unpaired; of these: 1054598 (5.69%) aligned 0 times 12136179 (65.46%) aligned exactly 1 time 5347814 (28.85%) aligned >1 times 94.31% overall alignment rate Time searching: 00:07:34 Overall time: 00:07:34 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] 12020656 / 17483993 = 0.6875 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 05:07:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.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 05:07:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:07:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:07:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.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 05:07:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:07:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:07:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.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 05:07:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:07:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:07:36: 1000000 INFO @ Mon, 03 Jun 2019 05:07:36: 1000000 INFO @ Mon, 03 Jun 2019 05:07:36: 1000000 INFO @ Mon, 03 Jun 2019 05:07:43: 2000000 INFO @ Mon, 03 Jun 2019 05:07:43: 2000000 INFO @ Mon, 03 Jun 2019 05:07:44: 2000000 INFO @ Mon, 03 Jun 2019 05:07:50: 3000000 INFO @ Mon, 03 Jun 2019 05:07:50: 3000000 INFO @ Mon, 03 Jun 2019 05:07:51: 3000000 INFO @ Mon, 03 Jun 2019 05:07:58: 4000000 INFO @ Mon, 03 Jun 2019 05:07:58: 4000000 INFO @ Mon, 03 Jun 2019 05:07:59: 4000000 INFO @ Mon, 03 Jun 2019 05:08:05: 5000000 INFO @ Mon, 03 Jun 2019 05:08:05: 5000000 INFO @ Mon, 03 Jun 2019 05:08:06: 5000000 INFO @ Mon, 03 Jun 2019 05:08:08: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:08:08: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:08:08: #1 total tags in treatment: 5463337 INFO @ Mon, 03 Jun 2019 05:08:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:08:08: #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 05:08:08: #1 tags after filtering in treatment: 5463337 INFO @ Mon, 03 Jun 2019 05:08:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:08:08: #1 finished! INFO @ Mon, 03 Jun 2019 05:08:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:08:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:08:08: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:08:08: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:08:08: #1 total tags in treatment: 5463337 INFO @ Mon, 03 Jun 2019 05:08:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:08:08: #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 05:08:09: #1 tags after filtering in treatment: 5463337 INFO @ Mon, 03 Jun 2019 05:08:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:08:09: #1 finished! INFO @ Mon, 03 Jun 2019 05:08:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:08:09: #2 number of paired peaks: 4740 INFO @ Mon, 03 Jun 2019 05:08:09: start model_add_line... INFO @ Mon, 03 Jun 2019 05:08:09: start X-correlation... INFO @ Mon, 03 Jun 2019 05:08:10: end of X-cor INFO @ Mon, 03 Jun 2019 05:08:10: #2 finished! INFO @ Mon, 03 Jun 2019 05:08:10: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 05:08:10: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 05:08:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.10_model.r INFO @ Mon, 03 Jun 2019 05:08:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:08:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:08:10: #2 number of paired peaks: 4740 INFO @ Mon, 03 Jun 2019 05:08:10: start model_add_line... INFO @ Mon, 03 Jun 2019 05:08:10: start X-correlation... INFO @ Mon, 03 Jun 2019 05:08:10: end of X-cor INFO @ Mon, 03 Jun 2019 05:08:10: #2 finished! INFO @ Mon, 03 Jun 2019 05:08:10: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 05:08:10: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 05:08:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.05_model.r INFO @ Mon, 03 Jun 2019 05:08:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:08:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:08:10: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:08:10: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:08:10: #1 total tags in treatment: 5463337 INFO @ Mon, 03 Jun 2019 05:08:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:08:10: #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 05:08:10: #1 tags after filtering in treatment: 5463337 INFO @ Mon, 03 Jun 2019 05:08:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:08:10: #1 finished! INFO @ Mon, 03 Jun 2019 05:08:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:08:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:08:11: #2 number of paired peaks: 4740 INFO @ Mon, 03 Jun 2019 05:08:11: start model_add_line... INFO @ Mon, 03 Jun 2019 05:08:11: start X-correlation... INFO @ Mon, 03 Jun 2019 05:08:11: end of X-cor INFO @ Mon, 03 Jun 2019 05:08:11: #2 finished! INFO @ Mon, 03 Jun 2019 05:08:11: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 05:08:11: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 03 Jun 2019 05:08:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.20_model.r INFO @ Mon, 03 Jun 2019 05:08:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:08:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:08:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:08:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:08:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:08:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:08:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:08:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:08:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.10_summits.bed INFO @ Mon, 03 Jun 2019 05:08:35: Done! INFO @ Mon, 03 Jun 2019 05:08:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:08:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.05_summits.bed pass1 - making usageList (15 chroms): 5 millis INFO @ Mon, 03 Jun 2019 05:08:35: Done! pass2 - checking and writing primary data (9780 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:08:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:08:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:08:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX187083/SRX187083.20_summits.bed INFO @ Mon, 03 Jun 2019 05:08:35: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (14076 records, 4 fields): 22 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5368 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。