Job ID = 1294400 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,387,357 reads read : 7,387,357 reads written : 7,387,357 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: 00:05:12 7387357 reads; of these: 7387357 (100.00%) were unpaired; of these: 166208 (2.25%) aligned 0 times 2869914 (38.85%) aligned exactly 1 time 4351235 (58.90%) aligned >1 times 97.75% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 1313095 / 7221149 = 0.1818 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 07:20:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.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 07:20:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:20:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:20:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.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 07:20:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:20:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:20:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.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 07:20:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:20:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:20:36: 1000000 INFO @ Mon, 03 Jun 2019 07:20:37: 1000000 INFO @ Mon, 03 Jun 2019 07:20:39: 1000000 INFO @ Mon, 03 Jun 2019 07:20:43: 2000000 INFO @ Mon, 03 Jun 2019 07:20:45: 2000000 INFO @ Mon, 03 Jun 2019 07:20:49: 2000000 INFO @ Mon, 03 Jun 2019 07:20:50: 3000000 INFO @ Mon, 03 Jun 2019 07:20:54: 3000000 INFO @ Mon, 03 Jun 2019 07:20:57: 4000000 INFO @ Mon, 03 Jun 2019 07:20:58: 3000000 INFO @ Mon, 03 Jun 2019 07:21:02: 4000000 INFO @ Mon, 03 Jun 2019 07:21:04: 5000000 INFO @ Mon, 03 Jun 2019 07:21:08: 4000000 INFO @ Mon, 03 Jun 2019 07:21:10: 5000000 INFO @ Mon, 03 Jun 2019 07:21:10: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 07:21:10: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 07:21:10: #1 total tags in treatment: 5908054 INFO @ Mon, 03 Jun 2019 07:21:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:21:10: #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 07:21:10: #1 tags after filtering in treatment: 5908054 INFO @ Mon, 03 Jun 2019 07:21:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:21:10: #1 finished! INFO @ Mon, 03 Jun 2019 07:21:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:21:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:21:11: #2 number of paired peaks: 1399 INFO @ Mon, 03 Jun 2019 07:21:11: start model_add_line... INFO @ Mon, 03 Jun 2019 07:21:11: start X-correlation... INFO @ Mon, 03 Jun 2019 07:21:11: end of X-cor INFO @ Mon, 03 Jun 2019 07:21:11: #2 finished! INFO @ Mon, 03 Jun 2019 07:21:11: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 07:21:11: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 07:21:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.10_model.r WARNING @ Mon, 03 Jun 2019 07:21:11: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:21:11: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 07:21:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 07:21:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:21:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:21:17: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 07:21:17: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 07:21:17: #1 total tags in treatment: 5908054 INFO @ Mon, 03 Jun 2019 07:21:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:21:17: #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 07:21:17: 5000000 INFO @ Mon, 03 Jun 2019 07:21:17: #1 tags after filtering in treatment: 5908054 INFO @ Mon, 03 Jun 2019 07:21:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:21:17: #1 finished! INFO @ Mon, 03 Jun 2019 07:21:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:21:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:21:18: #2 number of paired peaks: 1399 INFO @ Mon, 03 Jun 2019 07:21:18: start model_add_line... INFO @ Mon, 03 Jun 2019 07:21:18: start X-correlation... INFO @ Mon, 03 Jun 2019 07:21:18: end of X-cor INFO @ Mon, 03 Jun 2019 07:21:18: #2 finished! INFO @ Mon, 03 Jun 2019 07:21:18: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 07:21:18: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 07:21:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.20_model.r WARNING @ Mon, 03 Jun 2019 07:21:18: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:21:18: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 07:21:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 07:21:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:21:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:21:26: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 07:21:26: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 07:21:26: #1 total tags in treatment: 5908054 INFO @ Mon, 03 Jun 2019 07:21:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:21:26: #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 07:21:26: #1 tags after filtering in treatment: 5908054 INFO @ Mon, 03 Jun 2019 07:21:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:21:26: #1 finished! INFO @ Mon, 03 Jun 2019 07:21:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:21:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:21:27: #2 number of paired peaks: 1399 INFO @ Mon, 03 Jun 2019 07:21:27: start model_add_line... INFO @ Mon, 03 Jun 2019 07:21:27: start X-correlation... INFO @ Mon, 03 Jun 2019 07:21:27: end of X-cor INFO @ Mon, 03 Jun 2019 07:21:27: #2 finished! INFO @ Mon, 03 Jun 2019 07:21:27: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 07:21:27: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 07:21:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.05_model.r WARNING @ Mon, 03 Jun 2019 07:21:27: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 07:21:27: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 07:21:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 07:21:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:21:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:21:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:21:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:21:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:21:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:21:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.10_summits.bed INFO @ Mon, 03 Jun 2019 07:21:37: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2579 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:21:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:21:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:21:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:21:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.20_summits.bed INFO @ Mon, 03 Jun 2019 07:21:45: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1604 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:21:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:21:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:21:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287574/SRX287574.05_summits.bed INFO @ Mon, 03 Jun 2019 07:21:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3782 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。