Job ID = 1294609 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,822,900 reads read : 14,822,900 reads written : 14,822,900 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: 00:06:26 14822900 reads; of these: 14822900 (100.00%) were unpaired; of these: 808738 (5.46%) aligned 0 times 9789184 (66.04%) aligned exactly 1 time 4224978 (28.50%) aligned >1 times 94.54% overall alignment rate Time searching: 00:06:26 Overall time: 00:06:26 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] 1845697 / 14014162 = 0.1317 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 09:31:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.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 09:31:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:31:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:31:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.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 09:31:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:31:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:31:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.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 09:31:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:31:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:31:22: 1000000 INFO @ Mon, 03 Jun 2019 09:31:23: 1000000 INFO @ Mon, 03 Jun 2019 09:31:23: 1000000 INFO @ Mon, 03 Jun 2019 09:31:31: 2000000 INFO @ Mon, 03 Jun 2019 09:31:32: 2000000 INFO @ Mon, 03 Jun 2019 09:31:32: 2000000 INFO @ Mon, 03 Jun 2019 09:31:38: 3000000 INFO @ Mon, 03 Jun 2019 09:31:40: 3000000 INFO @ Mon, 03 Jun 2019 09:31:40: 3000000 INFO @ Mon, 03 Jun 2019 09:31:46: 4000000 INFO @ Mon, 03 Jun 2019 09:31:48: 4000000 INFO @ Mon, 03 Jun 2019 09:31:48: 4000000 INFO @ Mon, 03 Jun 2019 09:31:54: 5000000 INFO @ Mon, 03 Jun 2019 09:31:56: 5000000 INFO @ Mon, 03 Jun 2019 09:31:56: 5000000 INFO @ Mon, 03 Jun 2019 09:32:02: 6000000 INFO @ Mon, 03 Jun 2019 09:32:04: 6000000 INFO @ Mon, 03 Jun 2019 09:32:05: 6000000 INFO @ Mon, 03 Jun 2019 09:32:10: 7000000 INFO @ Mon, 03 Jun 2019 09:32:13: 7000000 INFO @ Mon, 03 Jun 2019 09:32:13: 7000000 INFO @ Mon, 03 Jun 2019 09:32:18: 8000000 INFO @ Mon, 03 Jun 2019 09:32:21: 8000000 INFO @ Mon, 03 Jun 2019 09:32:21: 8000000 INFO @ Mon, 03 Jun 2019 09:32:25: 9000000 INFO @ Mon, 03 Jun 2019 09:32:29: 9000000 INFO @ Mon, 03 Jun 2019 09:32:29: 9000000 INFO @ Mon, 03 Jun 2019 09:32:33: 10000000 INFO @ Mon, 03 Jun 2019 09:32:37: 10000000 INFO @ Mon, 03 Jun 2019 09:32:38: 10000000 INFO @ Mon, 03 Jun 2019 09:32:41: 11000000 INFO @ Mon, 03 Jun 2019 09:32:45: 11000000 INFO @ Mon, 03 Jun 2019 09:32:46: 11000000 INFO @ Mon, 03 Jun 2019 09:32:50: 12000000 INFO @ Mon, 03 Jun 2019 09:32:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:32:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:32:51: #1 total tags in treatment: 12168465 INFO @ Mon, 03 Jun 2019 09:32:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:32:51: #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 09:32:51: #1 tags after filtering in treatment: 12168465 INFO @ Mon, 03 Jun 2019 09:32:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:32:51: #1 finished! INFO @ Mon, 03 Jun 2019 09:32:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:32:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:32:52: #2 number of paired peaks: 312 WARNING @ Mon, 03 Jun 2019 09:32:52: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Mon, 03 Jun 2019 09:32:52: start model_add_line... INFO @ Mon, 03 Jun 2019 09:32:52: start X-correlation... INFO @ Mon, 03 Jun 2019 09:32:52: end of X-cor INFO @ Mon, 03 Jun 2019 09:32:52: #2 finished! INFO @ Mon, 03 Jun 2019 09:32:52: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 09:32:52: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 09:32:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.20_model.r WARNING @ Mon, 03 Jun 2019 09:32:52: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:32:52: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 09:32:52: #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 09:32:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:32:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:32:53: 12000000 INFO @ Mon, 03 Jun 2019 09:32:54: 12000000 INFO @ Mon, 03 Jun 2019 09:32:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:32:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:32:55: #1 total tags in treatment: 12168465 INFO @ Mon, 03 Jun 2019 09:32:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:32:55: #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 09:32:55: #1 tags after filtering in treatment: 12168465 INFO @ Mon, 03 Jun 2019 09:32:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:32:55: #1 finished! INFO @ Mon, 03 Jun 2019 09:32:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:32:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:32:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:32:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:32:56: #1 total tags in treatment: 12168465 INFO @ Mon, 03 Jun 2019 09:32:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:32:56: #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 09:32:56: #1 tags after filtering in treatment: 12168465 INFO @ Mon, 03 Jun 2019 09:32:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:32:56: #1 finished! INFO @ Mon, 03 Jun 2019 09:32:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:32:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:32:56: #2 number of paired peaks: 312 WARNING @ Mon, 03 Jun 2019 09:32:56: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Mon, 03 Jun 2019 09:32:56: start model_add_line... INFO @ Mon, 03 Jun 2019 09:32:56: start X-correlation... INFO @ Mon, 03 Jun 2019 09:32:56: end of X-cor INFO @ Mon, 03 Jun 2019 09:32:56: #2 finished! INFO @ Mon, 03 Jun 2019 09:32:56: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 09:32:56: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 09:32:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.05_model.r WARNING @ Mon, 03 Jun 2019 09:32:56: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:32:56: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 09:32:56: #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 09:32:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:32:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:32:57: #2 number of paired peaks: 312 WARNING @ Mon, 03 Jun 2019 09:32:57: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Mon, 03 Jun 2019 09:32:57: start model_add_line... INFO @ Mon, 03 Jun 2019 09:32:57: start X-correlation... INFO @ Mon, 03 Jun 2019 09:32:57: end of X-cor INFO @ Mon, 03 Jun 2019 09:32:57: #2 finished! INFO @ Mon, 03 Jun 2019 09:32:57: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 09:32:57: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 09:32:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.10_model.r WARNING @ Mon, 03 Jun 2019 09:32:57: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:32:57: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 09:32:57: #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 09:32:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:32:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:33:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:33:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:33:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:33:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:33:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:33:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.20_summits.bed INFO @ Mon, 03 Jun 2019 09:33:42: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1062 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:33:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:33:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:33:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.05_summits.bed INFO @ Mon, 03 Jun 2019 09:33:46: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1593 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:33:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:33:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:33:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287776/SRX287776.10_summits.bed INFO @ Mon, 03 Jun 2019 09:33:46: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1356 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。