Job ID = 1293746 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,429,986 reads read : 16,429,986 reads written : 16,429,986 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: 00:12:16 16429986 reads; of these: 16429986 (100.00%) were unpaired; of these: 1244646 (7.58%) aligned 0 times 4339053 (26.41%) aligned exactly 1 time 10846287 (66.02%) aligned >1 times 92.42% overall alignment rate Time searching: 00:12:16 Overall time: 00:12:16 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] 3093752 / 15185340 = 0.2037 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 02:24:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.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 02:24:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:24:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:24:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.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 02:24:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:24:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:24:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.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 02:24:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:24:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:24:43: 1000000 INFO @ Mon, 03 Jun 2019 02:24:44: 1000000 INFO @ Mon, 03 Jun 2019 02:24:44: 1000000 INFO @ Mon, 03 Jun 2019 02:24:51: 2000000 INFO @ Mon, 03 Jun 2019 02:24:53: 2000000 INFO @ Mon, 03 Jun 2019 02:24:53: 2000000 INFO @ Mon, 03 Jun 2019 02:24:59: 3000000 INFO @ Mon, 03 Jun 2019 02:25:02: 3000000 INFO @ Mon, 03 Jun 2019 02:25:02: 3000000 INFO @ Mon, 03 Jun 2019 02:25:07: 4000000 INFO @ Mon, 03 Jun 2019 02:25:10: 4000000 INFO @ Mon, 03 Jun 2019 02:25:11: 4000000 INFO @ Mon, 03 Jun 2019 02:25:15: 5000000 INFO @ Mon, 03 Jun 2019 02:25:19: 5000000 INFO @ Mon, 03 Jun 2019 02:25:20: 5000000 INFO @ Mon, 03 Jun 2019 02:25:22: 6000000 INFO @ Mon, 03 Jun 2019 02:25:27: 6000000 INFO @ Mon, 03 Jun 2019 02:25:28: 6000000 INFO @ Mon, 03 Jun 2019 02:25:30: 7000000 INFO @ Mon, 03 Jun 2019 02:25:36: 7000000 INFO @ Mon, 03 Jun 2019 02:25:37: 7000000 INFO @ Mon, 03 Jun 2019 02:25:38: 8000000 INFO @ Mon, 03 Jun 2019 02:25:45: 8000000 INFO @ Mon, 03 Jun 2019 02:25:46: 8000000 INFO @ Mon, 03 Jun 2019 02:25:47: 9000000 INFO @ Mon, 03 Jun 2019 02:25:53: 9000000 INFO @ Mon, 03 Jun 2019 02:25:55: 9000000 INFO @ Mon, 03 Jun 2019 02:25:55: 10000000 INFO @ Mon, 03 Jun 2019 02:26:02: 10000000 INFO @ Mon, 03 Jun 2019 02:26:03: 11000000 INFO @ Mon, 03 Jun 2019 02:26:03: 10000000 INFO @ Mon, 03 Jun 2019 02:26:10: 11000000 INFO @ Mon, 03 Jun 2019 02:26:11: 12000000 INFO @ Mon, 03 Jun 2019 02:26:11: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:26:11: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:26:11: #1 total tags in treatment: 12091588 INFO @ Mon, 03 Jun 2019 02:26:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:26:11: #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 02:26:12: 11000000 INFO @ Mon, 03 Jun 2019 02:26:12: #1 tags after filtering in treatment: 12091588 INFO @ Mon, 03 Jun 2019 02:26:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:26:12: #1 finished! INFO @ Mon, 03 Jun 2019 02:26:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:26:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:26:13: #2 number of paired peaks: 1829 INFO @ Mon, 03 Jun 2019 02:26:13: start model_add_line... INFO @ Mon, 03 Jun 2019 02:26:13: start X-correlation... INFO @ Mon, 03 Jun 2019 02:26:13: end of X-cor INFO @ Mon, 03 Jun 2019 02:26:13: #2 finished! INFO @ Mon, 03 Jun 2019 02:26:13: #2 predicted fragment length is 82 bps INFO @ Mon, 03 Jun 2019 02:26:13: #2 alternative fragment length(s) may be 3,82 bps INFO @ Mon, 03 Jun 2019 02:26:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.05_model.r WARNING @ Mon, 03 Jun 2019 02:26:13: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:26:13: #2 You may need to consider one of the other alternative d(s): 3,82 WARNING @ Mon, 03 Jun 2019 02:26:13: #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 02:26:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:26:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:26:19: 12000000 INFO @ Mon, 03 Jun 2019 02:26:19: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:26:19: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:26:19: #1 total tags in treatment: 12091588 INFO @ Mon, 03 Jun 2019 02:26:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:26:19: #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 02:26:20: #1 tags after filtering in treatment: 12091588 INFO @ Mon, 03 Jun 2019 02:26:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:26:20: #1 finished! INFO @ Mon, 03 Jun 2019 02:26:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:26:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:26:20: 12000000 INFO @ Mon, 03 Jun 2019 02:26:21: #2 number of paired peaks: 1829 INFO @ Mon, 03 Jun 2019 02:26:21: start model_add_line... INFO @ Mon, 03 Jun 2019 02:26:21: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:26:21: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:26:21: #1 total tags in treatment: 12091588 INFO @ Mon, 03 Jun 2019 02:26:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:26:21: #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 02:26:21: start X-correlation... INFO @ Mon, 03 Jun 2019 02:26:21: end of X-cor INFO @ Mon, 03 Jun 2019 02:26:21: #2 finished! INFO @ Mon, 03 Jun 2019 02:26:21: #2 predicted fragment length is 82 bps INFO @ Mon, 03 Jun 2019 02:26:21: #2 alternative fragment length(s) may be 3,82 bps INFO @ Mon, 03 Jun 2019 02:26:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.20_model.r WARNING @ Mon, 03 Jun 2019 02:26:21: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:26:21: #2 You may need to consider one of the other alternative d(s): 3,82 WARNING @ Mon, 03 Jun 2019 02:26:21: #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 02:26:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:26:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:26:21: #1 tags after filtering in treatment: 12091588 INFO @ Mon, 03 Jun 2019 02:26:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:26:21: #1 finished! INFO @ Mon, 03 Jun 2019 02:26:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:26:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:26:23: #2 number of paired peaks: 1829 INFO @ Mon, 03 Jun 2019 02:26:23: start model_add_line... INFO @ Mon, 03 Jun 2019 02:26:23: start X-correlation... INFO @ Mon, 03 Jun 2019 02:26:23: end of X-cor INFO @ Mon, 03 Jun 2019 02:26:23: #2 finished! INFO @ Mon, 03 Jun 2019 02:26:23: #2 predicted fragment length is 82 bps INFO @ Mon, 03 Jun 2019 02:26:23: #2 alternative fragment length(s) may be 3,82 bps INFO @ Mon, 03 Jun 2019 02:26:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.10_model.r WARNING @ Mon, 03 Jun 2019 02:26:23: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:26:23: #2 You may need to consider one of the other alternative d(s): 3,82 WARNING @ Mon, 03 Jun 2019 02:26:23: #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 02:26:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:26:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:26:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:26:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:26:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:27:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:27:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:27:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.05_summits.bed INFO @ Mon, 03 Jun 2019 02:27:01: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8861 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.20_summits.bed INFO @ Mon, 03 Jun 2019 02:27:08: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (592 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:27:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:27:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:27:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120692/SRX1120692.10_summits.bed INFO @ Mon, 03 Jun 2019 02:27:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2407 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。