Job ID = 1294591 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,131,262 reads read : 17,131,262 reads written : 17,131,262 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:47 17131262 reads; of these: 17131262 (100.00%) were unpaired; of these: 804271 (4.69%) aligned 0 times 10736490 (62.67%) aligned exactly 1 time 5590501 (32.63%) aligned >1 times 95.31% overall alignment rate Time searching: 00:08:48 Overall time: 00:08:48 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] 2125620 / 16326991 = 0.1302 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 09:29:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.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 09:29:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:29:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:29:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.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 09:29:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:29:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:29:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.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 09:29:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:29:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:29:37: 1000000 INFO @ Mon, 03 Jun 2019 09:29:37: 1000000 INFO @ Mon, 03 Jun 2019 09:29:38: 1000000 INFO @ Mon, 03 Jun 2019 09:29:44: 2000000 INFO @ Mon, 03 Jun 2019 09:29:45: 2000000 INFO @ Mon, 03 Jun 2019 09:29:46: 2000000 INFO @ Mon, 03 Jun 2019 09:29:51: 3000000 INFO @ Mon, 03 Jun 2019 09:29:52: 3000000 INFO @ Mon, 03 Jun 2019 09:29:54: 3000000 INFO @ Mon, 03 Jun 2019 09:29:58: 4000000 INFO @ Mon, 03 Jun 2019 09:30:00: 4000000 INFO @ Mon, 03 Jun 2019 09:30:02: 4000000 INFO @ Mon, 03 Jun 2019 09:30:05: 5000000 INFO @ Mon, 03 Jun 2019 09:30:07: 5000000 INFO @ Mon, 03 Jun 2019 09:30:09: 5000000 INFO @ Mon, 03 Jun 2019 09:30:12: 6000000 INFO @ Mon, 03 Jun 2019 09:30:14: 6000000 INFO @ Mon, 03 Jun 2019 09:30:17: 6000000 INFO @ Mon, 03 Jun 2019 09:30:19: 7000000 INFO @ Mon, 03 Jun 2019 09:30:22: 7000000 INFO @ Mon, 03 Jun 2019 09:30:24: 7000000 INFO @ Mon, 03 Jun 2019 09:30:26: 8000000 INFO @ Mon, 03 Jun 2019 09:30:29: 8000000 INFO @ Mon, 03 Jun 2019 09:30:32: 8000000 INFO @ Mon, 03 Jun 2019 09:30:33: 9000000 INFO @ Mon, 03 Jun 2019 09:30:36: 9000000 INFO @ Mon, 03 Jun 2019 09:30:39: 9000000 INFO @ Mon, 03 Jun 2019 09:30:40: 10000000 INFO @ Mon, 03 Jun 2019 09:30:44: 10000000 INFO @ Mon, 03 Jun 2019 09:30:47: 11000000 INFO @ Mon, 03 Jun 2019 09:30:47: 10000000 INFO @ Mon, 03 Jun 2019 09:30:51: 11000000 INFO @ Mon, 03 Jun 2019 09:30:53: 12000000 INFO @ Mon, 03 Jun 2019 09:30:55: 11000000 INFO @ Mon, 03 Jun 2019 09:30:58: 12000000 INFO @ Mon, 03 Jun 2019 09:31:00: 13000000 INFO @ Mon, 03 Jun 2019 09:31:02: 12000000 INFO @ Mon, 03 Jun 2019 09:31:06: 13000000 INFO @ Mon, 03 Jun 2019 09:31:07: 14000000 INFO @ Mon, 03 Jun 2019 09:31:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:31:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:31:09: #1 total tags in treatment: 14201371 INFO @ Mon, 03 Jun 2019 09:31:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:31:09: #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 09:31:09: #1 tags after filtering in treatment: 14201371 INFO @ Mon, 03 Jun 2019 09:31:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:31:09: #1 finished! INFO @ Mon, 03 Jun 2019 09:31:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:31:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:31:10: 13000000 INFO @ Mon, 03 Jun 2019 09:31:11: #2 number of paired peaks: 246 WARNING @ Mon, 03 Jun 2019 09:31:11: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 03 Jun 2019 09:31:11: start model_add_line... INFO @ Mon, 03 Jun 2019 09:31:11: start X-correlation... INFO @ Mon, 03 Jun 2019 09:31:11: end of X-cor INFO @ Mon, 03 Jun 2019 09:31:11: #2 finished! INFO @ Mon, 03 Jun 2019 09:31:11: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:31:11: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:31:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.10_model.r WARNING @ Mon, 03 Jun 2019 09:31:11: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:31:11: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:31:11: #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 09:31:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:31:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:31:13: 14000000 INFO @ Mon, 03 Jun 2019 09:31:15: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:31:15: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:31:15: #1 total tags in treatment: 14201371 INFO @ Mon, 03 Jun 2019 09:31:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:31:15: #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 09:31:15: #1 tags after filtering in treatment: 14201371 INFO @ Mon, 03 Jun 2019 09:31:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:31:15: #1 finished! INFO @ Mon, 03 Jun 2019 09:31:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:31:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:31:16: #2 number of paired peaks: 246 WARNING @ Mon, 03 Jun 2019 09:31:16: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 03 Jun 2019 09:31:16: start model_add_line... INFO @ Mon, 03 Jun 2019 09:31:16: start X-correlation... INFO @ Mon, 03 Jun 2019 09:31:16: end of X-cor INFO @ Mon, 03 Jun 2019 09:31:16: #2 finished! INFO @ Mon, 03 Jun 2019 09:31:16: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:31:16: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:31:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.05_model.r WARNING @ Mon, 03 Jun 2019 09:31:16: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:31:16: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:31:16: #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 09:31:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:31:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:31:17: 14000000 INFO @ Mon, 03 Jun 2019 09:31:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:31:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:31:19: #1 total tags in treatment: 14201371 INFO @ Mon, 03 Jun 2019 09:31:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:31:19: #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 09:31:19: #1 tags after filtering in treatment: 14201371 INFO @ Mon, 03 Jun 2019 09:31:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:31:19: #1 finished! INFO @ Mon, 03 Jun 2019 09:31:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:31:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:31:21: #2 number of paired peaks: 246 WARNING @ Mon, 03 Jun 2019 09:31:21: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 03 Jun 2019 09:31:21: start model_add_line... INFO @ Mon, 03 Jun 2019 09:31:21: start X-correlation... INFO @ Mon, 03 Jun 2019 09:31:21: end of X-cor INFO @ Mon, 03 Jun 2019 09:31:21: #2 finished! INFO @ Mon, 03 Jun 2019 09:31:21: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:31:21: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:31:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.20_model.r WARNING @ Mon, 03 Jun 2019 09:31:21: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:31:21: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:31:21: #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 09:31:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:31:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:31:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:31:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:31:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:32:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:32:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:32:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.10_summits.bed INFO @ Mon, 03 Jun 2019 09:32:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1748 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:32:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:32:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:32:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.05_summits.bed INFO @ Mon, 03 Jun 2019 09:32:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2181 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:32:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:32:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:32:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287764/SRX287764.20_summits.bed INFO @ Mon, 03 Jun 2019 09:32:17: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1350 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。