Job ID = 1294108 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,114,909 reads read : 22,114,909 reads written : 22,114,909 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: 00:06:52 22114909 reads; of these: 22114909 (100.00%) were unpaired; of these: 4718310 (21.34%) aligned 0 times 13509125 (61.09%) aligned exactly 1 time 3887474 (17.58%) aligned >1 times 78.66% overall alignment rate Time searching: 00:06:53 Overall time: 00:06:53 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] 11631563 / 17396599 = 0.6686 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 05:12:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.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 05:12:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:12:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:12:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.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 05:12:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:12:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:12:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.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 05:12:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:12:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:12:48: 1000000 INFO @ Mon, 03 Jun 2019 05:12:48: 1000000 INFO @ Mon, 03 Jun 2019 05:12:49: 1000000 INFO @ Mon, 03 Jun 2019 05:12:55: 2000000 INFO @ Mon, 03 Jun 2019 05:12:55: 2000000 INFO @ Mon, 03 Jun 2019 05:12:57: 2000000 INFO @ Mon, 03 Jun 2019 05:13:03: 3000000 INFO @ Mon, 03 Jun 2019 05:13:03: 3000000 INFO @ Mon, 03 Jun 2019 05:13:05: 3000000 INFO @ Mon, 03 Jun 2019 05:13:10: 4000000 INFO @ Mon, 03 Jun 2019 05:13:11: 4000000 INFO @ Mon, 03 Jun 2019 05:13:14: 4000000 INFO @ Mon, 03 Jun 2019 05:13:18: 5000000 INFO @ Mon, 03 Jun 2019 05:13:18: 5000000 INFO @ Mon, 03 Jun 2019 05:13:22: 5000000 INFO @ Mon, 03 Jun 2019 05:13:24: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:13:24: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:13:24: #1 total tags in treatment: 5765036 INFO @ Mon, 03 Jun 2019 05:13:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:13:24: #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 05:13:24: #1 tags after filtering in treatment: 5765036 INFO @ Mon, 03 Jun 2019 05:13:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:13:24: #1 finished! INFO @ Mon, 03 Jun 2019 05:13:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:13:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:13:24: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:13:24: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:13:24: #1 total tags in treatment: 5765036 INFO @ Mon, 03 Jun 2019 05:13:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:13:24: #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 05:13:24: #1 tags after filtering in treatment: 5765036 INFO @ Mon, 03 Jun 2019 05:13:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:13:24: #1 finished! INFO @ Mon, 03 Jun 2019 05:13:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:13:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:13:24: #2 number of paired peaks: 725 WARNING @ Mon, 03 Jun 2019 05:13:24: Fewer paired peaks (725) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 725 pairs to build model! INFO @ Mon, 03 Jun 2019 05:13:24: start model_add_line... INFO @ Mon, 03 Jun 2019 05:13:25: start X-correlation... INFO @ Mon, 03 Jun 2019 05:13:25: end of X-cor INFO @ Mon, 03 Jun 2019 05:13:25: #2 finished! INFO @ Mon, 03 Jun 2019 05:13:25: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 05:13:25: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 05:13:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.20_model.r WARNING @ Mon, 03 Jun 2019 05:13:25: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:13:25: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Mon, 03 Jun 2019 05:13:25: #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 05:13:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:13:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:13:25: #2 number of paired peaks: 725 WARNING @ Mon, 03 Jun 2019 05:13:25: Fewer paired peaks (725) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 725 pairs to build model! INFO @ Mon, 03 Jun 2019 05:13:25: start model_add_line... INFO @ Mon, 03 Jun 2019 05:13:25: start X-correlation... INFO @ Mon, 03 Jun 2019 05:13:25: end of X-cor INFO @ Mon, 03 Jun 2019 05:13:25: #2 finished! INFO @ Mon, 03 Jun 2019 05:13:25: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 05:13:25: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 05:13:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.10_model.r WARNING @ Mon, 03 Jun 2019 05:13:25: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:13:25: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Mon, 03 Jun 2019 05:13:25: #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 05:13:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:13:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:13:28: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:13:28: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:13:28: #1 total tags in treatment: 5765036 INFO @ Mon, 03 Jun 2019 05:13:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:13:28: #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 05:13:28: #1 tags after filtering in treatment: 5765036 INFO @ Mon, 03 Jun 2019 05:13:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:13:28: #1 finished! INFO @ Mon, 03 Jun 2019 05:13:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:13:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:13:29: #2 number of paired peaks: 725 WARNING @ Mon, 03 Jun 2019 05:13:29: Fewer paired peaks (725) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 725 pairs to build model! INFO @ Mon, 03 Jun 2019 05:13:29: start model_add_line... INFO @ Mon, 03 Jun 2019 05:13:29: start X-correlation... INFO @ Mon, 03 Jun 2019 05:13:29: end of X-cor INFO @ Mon, 03 Jun 2019 05:13:29: #2 finished! INFO @ Mon, 03 Jun 2019 05:13:29: #2 predicted fragment length is 84 bps INFO @ Mon, 03 Jun 2019 05:13:29: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 03 Jun 2019 05:13:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.05_model.r WARNING @ Mon, 03 Jun 2019 05:13:29: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:13:29: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Mon, 03 Jun 2019 05:13:29: #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 05:13:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:13:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:13:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:13:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:13:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:13:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:13:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:13:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.20_summits.bed INFO @ Mon, 03 Jun 2019 05:13:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (949 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:13:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:13:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:13:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.10_summits.bed INFO @ Mon, 03 Jun 2019 05:13:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1848 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:13:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:13:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:13:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX186113/SRX186113.05_summits.bed INFO @ Mon, 03 Jun 2019 05:13:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3509 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。