Job ID = 1294019 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,576,426 reads read : 11,152,852 reads written : 5,576,426 reads 0-length : 5,576,426 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: 00:06:39 5576426 reads; of these: 5576426 (100.00%) were unpaired; of these: 1823214 (32.70%) aligned 0 times 2723335 (48.84%) aligned exactly 1 time 1029877 (18.47%) aligned >1 times 67.30% overall alignment rate Time searching: 00:06:40 Overall time: 00:06:40 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] 96462 / 3753212 = 0.0257 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 04:23:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.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 04:23:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:23:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:23:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.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 04:23:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:23:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:23:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.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 04:23:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:23:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:23:48: 1000000 INFO @ Mon, 03 Jun 2019 04:23:48: 1000000 INFO @ Mon, 03 Jun 2019 04:23:52: 1000000 INFO @ Mon, 03 Jun 2019 04:24:01: 2000000 INFO @ Mon, 03 Jun 2019 04:24:01: 2000000 INFO @ Mon, 03 Jun 2019 04:24:09: 2000000 INFO @ Mon, 03 Jun 2019 04:24:15: 3000000 INFO @ Mon, 03 Jun 2019 04:24:15: 3000000 INFO @ Mon, 03 Jun 2019 04:24:24: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 04:24:24: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 04:24:24: #1 total tags in treatment: 3656750 INFO @ Mon, 03 Jun 2019 04:24:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:24:24: #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 04:24:24: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 04:24:24: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 04:24:24: #1 total tags in treatment: 3656750 INFO @ Mon, 03 Jun 2019 04:24:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:24:24: #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 04:24:24: #1 tags after filtering in treatment: 3656750 INFO @ Mon, 03 Jun 2019 04:24:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:24:24: #1 finished! INFO @ Mon, 03 Jun 2019 04:24:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:24:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:24:24: #1 tags after filtering in treatment: 3656750 INFO @ Mon, 03 Jun 2019 04:24:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:24:24: #1 finished! INFO @ Mon, 03 Jun 2019 04:24:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:24:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:24:25: #2 number of paired peaks: 247 WARNING @ Mon, 03 Jun 2019 04:24:25: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Mon, 03 Jun 2019 04:24:25: start model_add_line... INFO @ Mon, 03 Jun 2019 04:24:25: #2 number of paired peaks: 247 WARNING @ Mon, 03 Jun 2019 04:24:25: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Mon, 03 Jun 2019 04:24:25: start model_add_line... INFO @ Mon, 03 Jun 2019 04:24:25: start X-correlation... INFO @ Mon, 03 Jun 2019 04:24:25: start X-correlation... INFO @ Mon, 03 Jun 2019 04:24:25: end of X-cor INFO @ Mon, 03 Jun 2019 04:24:25: #2 finished! INFO @ Mon, 03 Jun 2019 04:24:25: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 04:24:25: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 03 Jun 2019 04:24:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.10_model.r WARNING @ Mon, 03 Jun 2019 04:24:25: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:24:25: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Mon, 03 Jun 2019 04:24:25: #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 04:24:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:24:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:24:25: end of X-cor INFO @ Mon, 03 Jun 2019 04:24:25: #2 finished! INFO @ Mon, 03 Jun 2019 04:24:25: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 04:24:25: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 03 Jun 2019 04:24:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.05_model.r WARNING @ Mon, 03 Jun 2019 04:24:25: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:24:25: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Mon, 03 Jun 2019 04:24:25: #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 04:24:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:24:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:24:27: 3000000 INFO @ Mon, 03 Jun 2019 04:24:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:24:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:24:38: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 04:24:38: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 04:24:38: #1 total tags in treatment: 3656750 INFO @ Mon, 03 Jun 2019 04:24:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:24:38: #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 04:24:38: #1 tags after filtering in treatment: 3656750 INFO @ Mon, 03 Jun 2019 04:24:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:24:38: #1 finished! INFO @ Mon, 03 Jun 2019 04:24:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:24:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:24:38: #2 number of paired peaks: 247 WARNING @ Mon, 03 Jun 2019 04:24:38: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Mon, 03 Jun 2019 04:24:38: start model_add_line... INFO @ Mon, 03 Jun 2019 04:24:39: start X-correlation... INFO @ Mon, 03 Jun 2019 04:24:39: end of X-cor INFO @ Mon, 03 Jun 2019 04:24:39: #2 finished! INFO @ Mon, 03 Jun 2019 04:24:39: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 04:24:39: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 03 Jun 2019 04:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.20_model.r WARNING @ Mon, 03 Jun 2019 04:24:39: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:24:39: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Mon, 03 Jun 2019 04:24:39: #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 04:24:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:24:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:24:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:24:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.10_summits.bed INFO @ Mon, 03 Jun 2019 04:24:41: Done! INFO @ Mon, 03 Jun 2019 04:24:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:24:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:24:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.05_summits.bed INFO @ Mon, 03 Jun 2019 04:24:41: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (294 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (616 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:24:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:24:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:24:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:24:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1760697/SRX1760697.20_summits.bed INFO @ Mon, 03 Jun 2019 04:24:55: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (123 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。