Job ID = 1294196 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,968,813 reads read : 27,968,813 reads written : 27,968,813 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: 00:00:01 Multiseed full-index search: 00:09:44 27968813 reads; of these: 27968813 (100.00%) were unpaired; of these: 7271042 (26.00%) aligned 0 times 13968185 (49.94%) aligned exactly 1 time 6729586 (24.06%) aligned >1 times 74.00% overall alignment rate Time searching: 00:09:45 Overall time: 00:09:45 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] 11336807 / 20697771 = 0.5477 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 05:40:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.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 05:40:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:40:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:40:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.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 05:40:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:40:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:40:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.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 05:40:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:40:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:40:20: 1000000 INFO @ Mon, 03 Jun 2019 05:40:20: 1000000 INFO @ Mon, 03 Jun 2019 05:40:21: 1000000 INFO @ Mon, 03 Jun 2019 05:40:29: 2000000 INFO @ Mon, 03 Jun 2019 05:40:29: 2000000 INFO @ Mon, 03 Jun 2019 05:40:29: 2000000 INFO @ Mon, 03 Jun 2019 05:40:37: 3000000 INFO @ Mon, 03 Jun 2019 05:40:37: 3000000 INFO @ Mon, 03 Jun 2019 05:40:38: 3000000 INFO @ Mon, 03 Jun 2019 05:40:44: 4000000 INFO @ Mon, 03 Jun 2019 05:40:44: 4000000 INFO @ Mon, 03 Jun 2019 05:40:46: 4000000 INFO @ Mon, 03 Jun 2019 05:40:52: 5000000 INFO @ Mon, 03 Jun 2019 05:40:52: 5000000 INFO @ Mon, 03 Jun 2019 05:40:54: 5000000 INFO @ Mon, 03 Jun 2019 05:41:00: 6000000 INFO @ Mon, 03 Jun 2019 05:41:00: 6000000 INFO @ Mon, 03 Jun 2019 05:41:02: 6000000 INFO @ Mon, 03 Jun 2019 05:41:08: 7000000 INFO @ Mon, 03 Jun 2019 05:41:08: 7000000 INFO @ Mon, 03 Jun 2019 05:41:11: 7000000 INFO @ Mon, 03 Jun 2019 05:41:16: 8000000 INFO @ Mon, 03 Jun 2019 05:41:16: 8000000 INFO @ Mon, 03 Jun 2019 05:41:19: 8000000 INFO @ Mon, 03 Jun 2019 05:41:24: 9000000 INFO @ Mon, 03 Jun 2019 05:41:24: 9000000 INFO @ Mon, 03 Jun 2019 05:41:27: 9000000 INFO @ Mon, 03 Jun 2019 05:41:27: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 05:41:27: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 05:41:27: #1 total tags in treatment: 9360964 INFO @ Mon, 03 Jun 2019 05:41:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:41:27: #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 05:41:27: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 05:41:27: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 05:41:27: #1 total tags in treatment: 9360964 INFO @ Mon, 03 Jun 2019 05:41:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:41:27: #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 05:41:27: #1 tags after filtering in treatment: 9360964 INFO @ Mon, 03 Jun 2019 05:41:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:41:27: #1 finished! INFO @ Mon, 03 Jun 2019 05:41:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:41:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:41:27: #1 tags after filtering in treatment: 9360964 INFO @ Mon, 03 Jun 2019 05:41:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:41:27: #1 finished! INFO @ Mon, 03 Jun 2019 05:41:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:41:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:41:28: #2 number of paired peaks: 776 WARNING @ Mon, 03 Jun 2019 05:41:28: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Mon, 03 Jun 2019 05:41:28: start model_add_line... INFO @ Mon, 03 Jun 2019 05:41:28: #2 number of paired peaks: 776 WARNING @ Mon, 03 Jun 2019 05:41:28: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Mon, 03 Jun 2019 05:41:28: start model_add_line... INFO @ Mon, 03 Jun 2019 05:41:28: start X-correlation... INFO @ Mon, 03 Jun 2019 05:41:29: start X-correlation... INFO @ Mon, 03 Jun 2019 05:41:29: end of X-cor INFO @ Mon, 03 Jun 2019 05:41:29: #2 finished! INFO @ Mon, 03 Jun 2019 05:41:29: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 05:41:29: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 05:41:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.10_model.r WARNING @ Mon, 03 Jun 2019 05:41:29: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:41:29: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 05:41:29: #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 05:41:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:41:29: end of X-cor INFO @ Mon, 03 Jun 2019 05:41:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:41:29: #2 finished! INFO @ Mon, 03 Jun 2019 05:41:29: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 05:41:29: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 05:41:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.20_model.r WARNING @ Mon, 03 Jun 2019 05:41:29: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:41:29: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 05:41:29: #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 05:41:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:41:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:41:30: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 05:41:30: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 05:41:30: #1 total tags in treatment: 9360964 INFO @ Mon, 03 Jun 2019 05:41:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:41:30: #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 05:41:30: #1 tags after filtering in treatment: 9360964 INFO @ Mon, 03 Jun 2019 05:41:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:41:30: #1 finished! INFO @ Mon, 03 Jun 2019 05:41:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:41:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:41:31: #2 number of paired peaks: 776 WARNING @ Mon, 03 Jun 2019 05:41:31: Fewer paired peaks (776) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 776 pairs to build model! INFO @ Mon, 03 Jun 2019 05:41:31: start model_add_line... INFO @ Mon, 03 Jun 2019 05:41:31: start X-correlation... INFO @ Mon, 03 Jun 2019 05:41:31: end of X-cor INFO @ Mon, 03 Jun 2019 05:41:31: #2 finished! INFO @ Mon, 03 Jun 2019 05:41:31: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 05:41:31: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 05:41:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.05_model.r WARNING @ Mon, 03 Jun 2019 05:41:31: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:41:31: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 05:41:31: #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 05:41:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:41:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:41:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:41:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:41:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:42:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:42:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:42:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.20_summits.bed INFO @ Mon, 03 Jun 2019 05:42:09: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1108 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:42:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:42:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:42:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.10_summits.bed INFO @ Mon, 03 Jun 2019 05:42:09: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1762 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:42:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:42:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:42:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197581/SRX197581.05_summits.bed INFO @ Mon, 03 Jun 2019 05:42:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3172 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。