Job ID = 1293745 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,690,855 reads read : 15,690,855 reads written : 15,690,855 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: 00:11:37 15690855 reads; of these: 15690855 (100.00%) were unpaired; of these: 1079273 (6.88%) aligned 0 times 4684951 (29.86%) aligned exactly 1 time 9926631 (63.26%) aligned >1 times 93.12% overall alignment rate Time searching: 00:11:37 Overall time: 00:11:37 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] 3464961 / 14611582 = 0.2371 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 02:23:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.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 02:23:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:23:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:23:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.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 02:23:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:23:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:23:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.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 02:23:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:23:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:23:27: 1000000 INFO @ Mon, 03 Jun 2019 02:23:27: 1000000 INFO @ Mon, 03 Jun 2019 02:23:27: 1000000 INFO @ Mon, 03 Jun 2019 02:23:37: 2000000 INFO @ Mon, 03 Jun 2019 02:23:38: 2000000 INFO @ Mon, 03 Jun 2019 02:23:38: 2000000 INFO @ Mon, 03 Jun 2019 02:23:48: 3000000 INFO @ Mon, 03 Jun 2019 02:23:49: 3000000 INFO @ Mon, 03 Jun 2019 02:23:49: 3000000 INFO @ Mon, 03 Jun 2019 02:23:58: 4000000 INFO @ Mon, 03 Jun 2019 02:24:00: 4000000 INFO @ Mon, 03 Jun 2019 02:24:00: 4000000 INFO @ Mon, 03 Jun 2019 02:24:09: 5000000 INFO @ Mon, 03 Jun 2019 02:24:12: 5000000 INFO @ Mon, 03 Jun 2019 02:24:12: 5000000 INFO @ Mon, 03 Jun 2019 02:24:19: 6000000 INFO @ Mon, 03 Jun 2019 02:24:23: 6000000 INFO @ Mon, 03 Jun 2019 02:24:23: 6000000 INFO @ Mon, 03 Jun 2019 02:24:29: 7000000 INFO @ Mon, 03 Jun 2019 02:24:34: 7000000 INFO @ Mon, 03 Jun 2019 02:24:34: 7000000 INFO @ Mon, 03 Jun 2019 02:24:40: 8000000 INFO @ Mon, 03 Jun 2019 02:24:45: 8000000 INFO @ Mon, 03 Jun 2019 02:24:45: 8000000 INFO @ Mon, 03 Jun 2019 02:24:50: 9000000 INFO @ Mon, 03 Jun 2019 02:24:56: 9000000 INFO @ Mon, 03 Jun 2019 02:24:56: 9000000 INFO @ Mon, 03 Jun 2019 02:25:00: 10000000 INFO @ Mon, 03 Jun 2019 02:25:08: 10000000 INFO @ Mon, 03 Jun 2019 02:25:08: 10000000 INFO @ Mon, 03 Jun 2019 02:25:11: 11000000 INFO @ Mon, 03 Jun 2019 02:25:12: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:25:12: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:25:12: #1 total tags in treatment: 11146621 INFO @ Mon, 03 Jun 2019 02:25:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:25:12: #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 02:25:12: #1 tags after filtering in treatment: 11146621 INFO @ Mon, 03 Jun 2019 02:25:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:25:12: #1 finished! INFO @ Mon, 03 Jun 2019 02:25:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:25:14: #2 number of paired peaks: 1366 INFO @ Mon, 03 Jun 2019 02:25:14: start model_add_line... INFO @ Mon, 03 Jun 2019 02:25:14: start X-correlation... INFO @ Mon, 03 Jun 2019 02:25:14: end of X-cor INFO @ Mon, 03 Jun 2019 02:25:14: #2 finished! INFO @ Mon, 03 Jun 2019 02:25:14: #2 predicted fragment length is 91 bps INFO @ Mon, 03 Jun 2019 02:25:14: #2 alternative fragment length(s) may be 3,91 bps INFO @ Mon, 03 Jun 2019 02:25:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.05_model.r WARNING @ Mon, 03 Jun 2019 02:25:14: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:25:14: #2 You may need to consider one of the other alternative d(s): 3,91 WARNING @ Mon, 03 Jun 2019 02:25:14: #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 02:25:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:25:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:25:19: 11000000 INFO @ Mon, 03 Jun 2019 02:25:19: 11000000 INFO @ Mon, 03 Jun 2019 02:25:20: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:25:20: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:25:20: #1 total tags in treatment: 11146621 INFO @ Mon, 03 Jun 2019 02:25:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:25:20: #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 02:25:20: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:25:20: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:25:20: #1 total tags in treatment: 11146621 INFO @ Mon, 03 Jun 2019 02:25:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:25:20: #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 02:25:21: #1 tags after filtering in treatment: 11146621 INFO @ Mon, 03 Jun 2019 02:25:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:25:21: #1 finished! INFO @ Mon, 03 Jun 2019 02:25:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:25:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:25:21: #1 tags after filtering in treatment: 11146621 INFO @ Mon, 03 Jun 2019 02:25:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:25:21: #1 finished! INFO @ Mon, 03 Jun 2019 02:25:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:25:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:25:22: #2 number of paired peaks: 1366 INFO @ Mon, 03 Jun 2019 02:25:22: start model_add_line... INFO @ Mon, 03 Jun 2019 02:25:22: #2 number of paired peaks: 1366 INFO @ Mon, 03 Jun 2019 02:25:22: start model_add_line... INFO @ Mon, 03 Jun 2019 02:25:22: start X-correlation... INFO @ Mon, 03 Jun 2019 02:25:22: end of X-cor INFO @ Mon, 03 Jun 2019 02:25:22: #2 finished! INFO @ Mon, 03 Jun 2019 02:25:22: #2 predicted fragment length is 91 bps INFO @ Mon, 03 Jun 2019 02:25:22: #2 alternative fragment length(s) may be 3,91 bps INFO @ Mon, 03 Jun 2019 02:25:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.20_model.r WARNING @ Mon, 03 Jun 2019 02:25:22: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:25:22: #2 You may need to consider one of the other alternative d(s): 3,91 WARNING @ Mon, 03 Jun 2019 02:25:22: #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 02:25:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:25:22: start X-correlation... INFO @ Mon, 03 Jun 2019 02:25:22: end of X-cor INFO @ Mon, 03 Jun 2019 02:25:22: #2 finished! INFO @ Mon, 03 Jun 2019 02:25:22: #2 predicted fragment length is 91 bps INFO @ Mon, 03 Jun 2019 02:25:22: #2 alternative fragment length(s) may be 3,91 bps INFO @ Mon, 03 Jun 2019 02:25:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.10_model.r WARNING @ Mon, 03 Jun 2019 02:25:22: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:25:22: #2 You may need to consider one of the other alternative d(s): 3,91 WARNING @ Mon, 03 Jun 2019 02:25:22: #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 02:25:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:25:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:25:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:25:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:25:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:25:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:25:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.05_summits.bed INFO @ Mon, 03 Jun 2019 02:25:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9496 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:26:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:26:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:26:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:26:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:26:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.20_summits.bed INFO @ Mon, 03 Jun 2019 02:26:08: Done! INFO @ Mon, 03 Jun 2019 02:26:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120691/SRX1120691.10_summits.bed INFO @ Mon, 03 Jun 2019 02:26:08: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (424 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2415 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。