Job ID = 2590329 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 38,885,479 reads read : 38,885,479 reads written : 38,885,479 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1027845.sra.cache’: 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: 00:13:49 38885479 reads; of these: 38885479 (100.00%) were unpaired; of these: 19284220 (49.59%) aligned 0 times 13303182 (34.21%) aligned exactly 1 time 6298077 (16.20%) aligned >1 times 50.41% overall alignment rate Time searching: 00:13:49 Overall time: 00:13:49 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] 11180045 / 19601259 = 0.5704 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, 12 Aug 2019 21:03:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.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, 12 Aug 2019 21:03:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:03:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:03:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.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, 12 Aug 2019 21:03:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:03:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:03:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.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, 12 Aug 2019 21:03:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:03:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:04:01: 1000000 INFO @ Mon, 12 Aug 2019 21:04:03: 1000000 INFO @ Mon, 12 Aug 2019 21:04:04: 1000000 INFO @ Mon, 12 Aug 2019 21:04:09: 2000000 INFO @ Mon, 12 Aug 2019 21:04:12: 2000000 INFO @ Mon, 12 Aug 2019 21:04:13: 2000000 INFO @ Mon, 12 Aug 2019 21:04:18: 3000000 INFO @ Mon, 12 Aug 2019 21:04:22: 3000000 INFO @ Mon, 12 Aug 2019 21:04:23: 3000000 INFO @ Mon, 12 Aug 2019 21:04:26: 4000000 INFO @ Mon, 12 Aug 2019 21:04:31: 4000000 INFO @ Mon, 12 Aug 2019 21:04:32: 4000000 INFO @ Mon, 12 Aug 2019 21:04:34: 5000000 INFO @ Mon, 12 Aug 2019 21:04:40: 5000000 INFO @ Mon, 12 Aug 2019 21:04:41: 5000000 INFO @ Mon, 12 Aug 2019 21:04:42: 6000000 INFO @ Mon, 12 Aug 2019 21:04:49: 6000000 INFO @ Mon, 12 Aug 2019 21:04:50: 7000000 INFO @ Mon, 12 Aug 2019 21:04:51: 6000000 INFO @ Mon, 12 Aug 2019 21:04:58: 7000000 INFO @ Mon, 12 Aug 2019 21:04:59: 8000000 INFO @ Mon, 12 Aug 2019 21:05:00: 7000000 INFO @ Mon, 12 Aug 2019 21:05:02: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:05:02: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:05:02: #1 total tags in treatment: 8421214 INFO @ Mon, 12 Aug 2019 21:05:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:05:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:05:02: #1 tags after filtering in treatment: 8421214 INFO @ Mon, 12 Aug 2019 21:05:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:05:02: #1 finished! INFO @ Mon, 12 Aug 2019 21:05:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:05:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:05:03: #2 number of paired peaks: 1454 INFO @ Mon, 12 Aug 2019 21:05:03: start model_add_line... INFO @ Mon, 12 Aug 2019 21:05:03: start X-correlation... INFO @ Mon, 12 Aug 2019 21:05:03: end of X-cor INFO @ Mon, 12 Aug 2019 21:05:03: #2 finished! INFO @ Mon, 12 Aug 2019 21:05:03: #2 predicted fragment length is 125 bps INFO @ Mon, 12 Aug 2019 21:05:03: #2 alternative fragment length(s) may be 125 bps INFO @ Mon, 12 Aug 2019 21:05:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.05_model.r INFO @ Mon, 12 Aug 2019 21:05:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:05:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:05:07: 8000000 INFO @ Mon, 12 Aug 2019 21:05:09: 8000000 INFO @ Mon, 12 Aug 2019 21:05:11: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:05:11: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:05:11: #1 total tags in treatment: 8421214 INFO @ Mon, 12 Aug 2019 21:05:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:05:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:05:11: #1 tags after filtering in treatment: 8421214 INFO @ Mon, 12 Aug 2019 21:05:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:05:11: #1 finished! INFO @ Mon, 12 Aug 2019 21:05:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:05:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:05:12: #2 number of paired peaks: 1454 INFO @ Mon, 12 Aug 2019 21:05:12: start model_add_line... INFO @ Mon, 12 Aug 2019 21:05:12: start X-correlation... INFO @ Mon, 12 Aug 2019 21:05:12: end of X-cor INFO @ Mon, 12 Aug 2019 21:05:12: #2 finished! INFO @ Mon, 12 Aug 2019 21:05:12: #2 predicted fragment length is 125 bps INFO @ Mon, 12 Aug 2019 21:05:12: #2 alternative fragment length(s) may be 125 bps INFO @ Mon, 12 Aug 2019 21:05:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.10_model.r INFO @ Mon, 12 Aug 2019 21:05:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:05:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:05:13: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:05:13: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:05:13: #1 total tags in treatment: 8421214 INFO @ Mon, 12 Aug 2019 21:05:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:05:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 21:05:13: #1 tags after filtering in treatment: 8421214 INFO @ Mon, 12 Aug 2019 21:05:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:05:13: #1 finished! INFO @ Mon, 12 Aug 2019 21:05:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:05:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:05:14: #2 number of paired peaks: 1454 INFO @ Mon, 12 Aug 2019 21:05:14: start model_add_line... INFO @ Mon, 12 Aug 2019 21:05:14: start X-correlation... INFO @ Mon, 12 Aug 2019 21:05:14: end of X-cor INFO @ Mon, 12 Aug 2019 21:05:14: #2 finished! INFO @ Mon, 12 Aug 2019 21:05:14: #2 predicted fragment length is 125 bps INFO @ Mon, 12 Aug 2019 21:05:14: #2 alternative fragment length(s) may be 125 bps INFO @ Mon, 12 Aug 2019 21:05:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.20_model.r INFO @ Mon, 12 Aug 2019 21:05:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:05:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:05:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:05:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:05:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:05:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:05:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:05:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.05_summits.bed INFO @ Mon, 12 Aug 2019 21:05:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5382 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:05:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:05:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:05:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.10_summits.bed INFO @ Mon, 12 Aug 2019 21:05:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3909 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:05:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:05:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:05:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX375355/SRX375355.20_summits.bed INFO @ Mon, 12 Aug 2019 21:05:52: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2723 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。