Job ID = 2590276 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,005,081 reads read : 24,005,081 reads written : 24,005,081 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR586011.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: 00:05:27 24005081 reads; of these: 24005081 (100.00%) were unpaired; of these: 19100524 (79.57%) aligned 0 times 2183997 (9.10%) aligned exactly 1 time 2720560 (11.33%) aligned >1 times 20.43% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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_rmdupse_core] 1774292 / 4904557 = 0.3618 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 20:31:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.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 20:31:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:31:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:31:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.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 20:31:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:31:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.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 20:31:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:31:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:31:15: 1000000 INFO @ Mon, 12 Aug 2019 20:31:17: 1000000 INFO @ Mon, 12 Aug 2019 20:31:17: 1000000 INFO @ Mon, 12 Aug 2019 20:31:23: 2000000 INFO @ Mon, 12 Aug 2019 20:31:26: 2000000 INFO @ Mon, 12 Aug 2019 20:31:27: 2000000 INFO @ Mon, 12 Aug 2019 20:31:31: 3000000 INFO @ Mon, 12 Aug 2019 20:31:32: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:31:32: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:31:32: #1 total tags in treatment: 3130265 INFO @ Mon, 12 Aug 2019 20:31:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:31:32: #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 20:31:32: #1 tags after filtering in treatment: 3130265 INFO @ Mon, 12 Aug 2019 20:31:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:31:32: #1 finished! INFO @ Mon, 12 Aug 2019 20:31:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:31:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:31:33: #2 number of paired peaks: 1236 INFO @ Mon, 12 Aug 2019 20:31:33: start model_add_line... INFO @ Mon, 12 Aug 2019 20:31:33: start X-correlation... INFO @ Mon, 12 Aug 2019 20:31:33: end of X-cor INFO @ Mon, 12 Aug 2019 20:31:33: #2 finished! INFO @ Mon, 12 Aug 2019 20:31:33: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 20:31:33: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 12 Aug 2019 20:31:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.05_model.r WARNING @ Mon, 12 Aug 2019 20:31:33: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:31:33: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 12 Aug 2019 20:31:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:31:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:31:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:31:34: 3000000 INFO @ Mon, 12 Aug 2019 20:31:35: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:31:35: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:31:35: #1 total tags in treatment: 3130265 INFO @ Mon, 12 Aug 2019 20:31:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:31:35: #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 20:31:35: #1 tags after filtering in treatment: 3130265 INFO @ Mon, 12 Aug 2019 20:31:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:31:35: #1 finished! INFO @ Mon, 12 Aug 2019 20:31:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:31:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:31:35: #2 number of paired peaks: 1236 INFO @ Mon, 12 Aug 2019 20:31:35: start model_add_line... INFO @ Mon, 12 Aug 2019 20:31:35: start X-correlation... INFO @ Mon, 12 Aug 2019 20:31:35: end of X-cor INFO @ Mon, 12 Aug 2019 20:31:35: #2 finished! INFO @ Mon, 12 Aug 2019 20:31:35: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 20:31:35: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 12 Aug 2019 20:31:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.20_model.r WARNING @ Mon, 12 Aug 2019 20:31:35: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:31:35: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 12 Aug 2019 20:31:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:31:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:31:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:31:37: 3000000 INFO @ Mon, 12 Aug 2019 20:31:38: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:31:38: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:31:38: #1 total tags in treatment: 3130265 INFO @ Mon, 12 Aug 2019 20:31:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:31:38: #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 20:31:38: #1 tags after filtering in treatment: 3130265 INFO @ Mon, 12 Aug 2019 20:31:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:31:38: #1 finished! INFO @ Mon, 12 Aug 2019 20:31:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:31:38: #2 number of paired peaks: 1236 INFO @ Mon, 12 Aug 2019 20:31:38: start model_add_line... INFO @ Mon, 12 Aug 2019 20:31:38: start X-correlation... INFO @ Mon, 12 Aug 2019 20:31:38: end of X-cor INFO @ Mon, 12 Aug 2019 20:31:38: #2 finished! INFO @ Mon, 12 Aug 2019 20:31:38: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 20:31:38: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 12 Aug 2019 20:31:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.10_model.r WARNING @ Mon, 12 Aug 2019 20:31:38: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:31:38: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 12 Aug 2019 20:31:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:31:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:31:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:31:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:31:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:31:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:31:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:31:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.05_summits.bed INFO @ Mon, 12 Aug 2019 20:31:47: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2437 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:31:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:31:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:31:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.20_summits.bed INFO @ Mon, 12 Aug 2019 20:31:49: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (821 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:31:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:31:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:31:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193633/SRX193633.10_summits.bed INFO @ Mon, 12 Aug 2019 20:31:52: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1397 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。