Job ID = 1294177 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,974,730 reads read : 22,974,730 reads written : 22,974,730 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: 00:05:31 22974730 reads; of these: 22974730 (100.00%) were unpaired; of these: 7693699 (33.49%) aligned 0 times 12768291 (55.58%) aligned exactly 1 time 2512740 (10.94%) aligned >1 times 66.51% overall alignment rate Time searching: 00:05:31 Overall time: 00:05:31 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] 3900597 / 15281031 = 0.2553 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 05:27:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.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 05:27:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:27:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:27:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.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 05:27:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:27:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:27:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.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 05:27:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:27:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:27:35: 1000000 INFO @ Mon, 03 Jun 2019 05:27:37: 1000000 INFO @ Mon, 03 Jun 2019 05:27:37: 1000000 INFO @ Mon, 03 Jun 2019 05:27:43: 2000000 INFO @ Mon, 03 Jun 2019 05:27:46: 2000000 INFO @ Mon, 03 Jun 2019 05:27:46: 2000000 INFO @ Mon, 03 Jun 2019 05:27:50: 3000000 INFO @ Mon, 03 Jun 2019 05:27:55: 3000000 INFO @ Mon, 03 Jun 2019 05:27:55: 3000000 INFO @ Mon, 03 Jun 2019 05:27:58: 4000000 INFO @ Mon, 03 Jun 2019 05:28:04: 4000000 INFO @ Mon, 03 Jun 2019 05:28:05: 4000000 INFO @ Mon, 03 Jun 2019 05:28:06: 5000000 INFO @ Mon, 03 Jun 2019 05:28:13: 5000000 INFO @ Mon, 03 Jun 2019 05:28:14: 6000000 INFO @ Mon, 03 Jun 2019 05:28:14: 5000000 INFO @ Mon, 03 Jun 2019 05:28:21: 7000000 INFO @ Mon, 03 Jun 2019 05:28:23: 6000000 INFO @ Mon, 03 Jun 2019 05:28:24: 6000000 INFO @ Mon, 03 Jun 2019 05:28:29: 8000000 INFO @ Mon, 03 Jun 2019 05:28:31: 7000000 INFO @ Mon, 03 Jun 2019 05:28:33: 7000000 INFO @ Mon, 03 Jun 2019 05:28:36: 9000000 INFO @ Mon, 03 Jun 2019 05:28:40: 8000000 INFO @ Mon, 03 Jun 2019 05:28:42: 8000000 INFO @ Mon, 03 Jun 2019 05:28:44: 10000000 INFO @ Mon, 03 Jun 2019 05:28:49: 9000000 INFO @ Mon, 03 Jun 2019 05:28:51: 9000000 INFO @ Mon, 03 Jun 2019 05:28:51: 11000000 INFO @ Mon, 03 Jun 2019 05:28:54: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:28:54: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:28:54: #1 total tags in treatment: 11380434 INFO @ Mon, 03 Jun 2019 05:28:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:28:54: #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 05:28:55: #1 tags after filtering in treatment: 11380434 INFO @ Mon, 03 Jun 2019 05:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:28:55: #1 finished! INFO @ Mon, 03 Jun 2019 05:28:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:28:56: #2 number of paired peaks: 5012 INFO @ Mon, 03 Jun 2019 05:28:56: start model_add_line... INFO @ Mon, 03 Jun 2019 05:28:56: start X-correlation... INFO @ Mon, 03 Jun 2019 05:28:56: end of X-cor INFO @ Mon, 03 Jun 2019 05:28:56: #2 finished! INFO @ Mon, 03 Jun 2019 05:28:56: #2 predicted fragment length is 80 bps INFO @ Mon, 03 Jun 2019 05:28:56: #2 alternative fragment length(s) may be 80 bps INFO @ Mon, 03 Jun 2019 05:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.10_model.r WARNING @ Mon, 03 Jun 2019 05:28:56: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:28:56: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Mon, 03 Jun 2019 05:28:56: #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 05:28:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:28:58: 10000000 INFO @ Mon, 03 Jun 2019 05:29:00: 10000000 INFO @ Mon, 03 Jun 2019 05:29:06: 11000000 INFO @ Mon, 03 Jun 2019 05:29:09: 11000000 INFO @ Mon, 03 Jun 2019 05:29:10: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:29:10: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:29:10: #1 total tags in treatment: 11380434 INFO @ Mon, 03 Jun 2019 05:29:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:29:10: #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 05:29:10: #1 tags after filtering in treatment: 11380434 INFO @ Mon, 03 Jun 2019 05:29:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:29:10: #1 finished! INFO @ Mon, 03 Jun 2019 05:29:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:29:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:29:12: #2 number of paired peaks: 5012 INFO @ Mon, 03 Jun 2019 05:29:12: start model_add_line... INFO @ Mon, 03 Jun 2019 05:29:12: start X-correlation... INFO @ Mon, 03 Jun 2019 05:29:12: end of X-cor INFO @ Mon, 03 Jun 2019 05:29:12: #2 finished! INFO @ Mon, 03 Jun 2019 05:29:12: #2 predicted fragment length is 80 bps INFO @ Mon, 03 Jun 2019 05:29:12: #2 alternative fragment length(s) may be 80 bps INFO @ Mon, 03 Jun 2019 05:29:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.20_model.r WARNING @ Mon, 03 Jun 2019 05:29:12: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:29:12: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Mon, 03 Jun 2019 05:29:12: #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 05:29:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:29:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:29:12: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:29:12: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:29:12: #1 total tags in treatment: 11380434 INFO @ Mon, 03 Jun 2019 05:29:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:29:12: #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 05:29:13: #1 tags after filtering in treatment: 11380434 INFO @ Mon, 03 Jun 2019 05:29:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:29:13: #1 finished! INFO @ Mon, 03 Jun 2019 05:29:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:29:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:29:14: #2 number of paired peaks: 5012 INFO @ Mon, 03 Jun 2019 05:29:14: start model_add_line... INFO @ Mon, 03 Jun 2019 05:29:14: start X-correlation... INFO @ Mon, 03 Jun 2019 05:29:14: end of X-cor INFO @ Mon, 03 Jun 2019 05:29:14: #2 finished! INFO @ Mon, 03 Jun 2019 05:29:14: #2 predicted fragment length is 80 bps INFO @ Mon, 03 Jun 2019 05:29:14: #2 alternative fragment length(s) may be 80 bps INFO @ Mon, 03 Jun 2019 05:29:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.05_model.r WARNING @ Mon, 03 Jun 2019 05:29:14: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:29:14: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Mon, 03 Jun 2019 05:29:14: #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 05:29:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:29:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:29:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:29:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:29:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:29:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:29:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.10_summits.bed INFO @ Mon, 03 Jun 2019 05:29:46: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6196 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:29:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:30:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:30:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:30:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.20_summits.bed INFO @ Mon, 03 Jun 2019 05:30:00: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5099 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:30:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:30:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:30:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197565/SRX197565.05_summits.bed INFO @ Mon, 03 Jun 2019 05:30:05: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7099 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。