Job ID = 1294553 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,077,644 reads read : 9,077,644 reads written : 9,077,644 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: 00:04:21 9077644 reads; of these: 9077644 (100.00%) were unpaired; of these: 341429 (3.76%) aligned 0 times 5891697 (64.90%) aligned exactly 1 time 2844518 (31.34%) aligned >1 times 96.24% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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_rmdupse_core] 1437451 / 8736215 = 0.1645 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 09:00:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.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 09:00:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:00:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:00:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.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 09:00:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:00:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:00:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.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 09:00:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:00:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:00:40: 1000000 INFO @ Mon, 03 Jun 2019 09:00:41: 1000000 INFO @ Mon, 03 Jun 2019 09:00:41: 1000000 INFO @ Mon, 03 Jun 2019 09:00:48: 2000000 INFO @ Mon, 03 Jun 2019 09:00:49: 2000000 INFO @ Mon, 03 Jun 2019 09:00:49: 2000000 INFO @ Mon, 03 Jun 2019 09:00:55: 3000000 INFO @ Mon, 03 Jun 2019 09:00:58: 3000000 INFO @ Mon, 03 Jun 2019 09:00:58: 3000000 INFO @ Mon, 03 Jun 2019 09:01:03: 4000000 INFO @ Mon, 03 Jun 2019 09:01:06: 4000000 INFO @ Mon, 03 Jun 2019 09:01:06: 4000000 INFO @ Mon, 03 Jun 2019 09:01:11: 5000000 INFO @ Mon, 03 Jun 2019 09:01:15: 5000000 INFO @ Mon, 03 Jun 2019 09:01:15: 5000000 INFO @ Mon, 03 Jun 2019 09:01:18: 6000000 INFO @ Mon, 03 Jun 2019 09:01:23: 6000000 INFO @ Mon, 03 Jun 2019 09:01:23: 6000000 INFO @ Mon, 03 Jun 2019 09:01:26: 7000000 INFO @ Mon, 03 Jun 2019 09:01:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:01:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:01:28: #1 total tags in treatment: 7298764 INFO @ Mon, 03 Jun 2019 09:01:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:01:28: #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 09:01:28: #1 tags after filtering in treatment: 7298764 INFO @ Mon, 03 Jun 2019 09:01:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:01:28: #1 finished! INFO @ Mon, 03 Jun 2019 09:01:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:01:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:01:29: #2 number of paired peaks: 623 WARNING @ Mon, 03 Jun 2019 09:01:29: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Mon, 03 Jun 2019 09:01:29: start model_add_line... INFO @ Mon, 03 Jun 2019 09:01:29: start X-correlation... INFO @ Mon, 03 Jun 2019 09:01:29: end of X-cor INFO @ Mon, 03 Jun 2019 09:01:29: #2 finished! INFO @ Mon, 03 Jun 2019 09:01:29: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:01:29: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:01:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.10_model.r WARNING @ Mon, 03 Jun 2019 09:01:29: #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 09:01:29: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:01:29: #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 09:01:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:01:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:01:32: 7000000 INFO @ Mon, 03 Jun 2019 09:01:32: 7000000 INFO @ Mon, 03 Jun 2019 09:01:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:01:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:01:34: #1 total tags in treatment: 7298764 INFO @ Mon, 03 Jun 2019 09:01:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:01:34: #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 09:01:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:01:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:01:34: #1 total tags in treatment: 7298764 INFO @ Mon, 03 Jun 2019 09:01:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:01:34: #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 09:01:35: #1 tags after filtering in treatment: 7298764 INFO @ Mon, 03 Jun 2019 09:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:01:35: #1 finished! INFO @ Mon, 03 Jun 2019 09:01:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:01:35: #1 tags after filtering in treatment: 7298764 INFO @ Mon, 03 Jun 2019 09:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:01:35: #1 finished! INFO @ Mon, 03 Jun 2019 09:01:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:01:35: #2 number of paired peaks: 623 WARNING @ Mon, 03 Jun 2019 09:01:35: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Mon, 03 Jun 2019 09:01:35: start model_add_line... INFO @ Mon, 03 Jun 2019 09:01:35: #2 number of paired peaks: 623 WARNING @ Mon, 03 Jun 2019 09:01:35: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Mon, 03 Jun 2019 09:01:35: start model_add_line... INFO @ Mon, 03 Jun 2019 09:01:35: start X-correlation... INFO @ Mon, 03 Jun 2019 09:01:35: start X-correlation... INFO @ Mon, 03 Jun 2019 09:01:35: end of X-cor INFO @ Mon, 03 Jun 2019 09:01:35: #2 finished! INFO @ Mon, 03 Jun 2019 09:01:35: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:01:35: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:01:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.20_model.r INFO @ Mon, 03 Jun 2019 09:01:35: end of X-cor INFO @ Mon, 03 Jun 2019 09:01:35: #2 finished! INFO @ Mon, 03 Jun 2019 09:01:35: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:01:35: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:01:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.05_model.r WARNING @ Mon, 03 Jun 2019 09:01:35: #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 09:01:35: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:01:35: #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 09:01:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:01:35: #3 Pre-compute pvalue-qvalue table... WARNING @ Mon, 03 Jun 2019 09:01:35: #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 09:01:35: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:01:35: #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 09:01:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:01:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:01:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:01:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:01:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:02:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:02:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:02:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.10_summits.bed INFO @ Mon, 03 Jun 2019 09:02:01: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1824 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:02:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:02:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:02:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.05_summits.bed INFO @ Mon, 03 Jun 2019 09:02:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:02:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:02:07: Done! INFO @ Mon, 03 Jun 2019 09:02:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287739/SRX287739.20_summits.bed INFO @ Mon, 03 Jun 2019 09:02:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1235 records, 4 fields): 6 millis pass1 - making usageList (14 chroms): 2 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (3258 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。