Job ID = 1293749 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,959,058 reads read : 6,959,058 reads written : 6,959,058 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: 00:02:25 6959058 reads; of these: 6959058 (100.00%) were unpaired; of these: 2703532 (38.85%) aligned 0 times 3597592 (51.70%) aligned exactly 1 time 657934 (9.45%) aligned >1 times 61.15% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 111704 / 4255526 = 0.0262 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 02:11:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.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 02:11:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:11:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:11:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.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 02:11:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:11:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:11:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.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 02:11:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:11:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:11:44: 1000000 INFO @ Mon, 03 Jun 2019 02:11:44: 1000000 INFO @ Mon, 03 Jun 2019 02:11:44: 1000000 INFO @ Mon, 03 Jun 2019 02:11:57: 2000000 INFO @ Mon, 03 Jun 2019 02:11:57: 2000000 INFO @ Mon, 03 Jun 2019 02:11:57: 2000000 INFO @ Mon, 03 Jun 2019 02:12:09: 3000000 INFO @ Mon, 03 Jun 2019 02:12:10: 3000000 INFO @ Mon, 03 Jun 2019 02:12:10: 3000000 INFO @ Mon, 03 Jun 2019 02:12:21: 4000000 INFO @ Mon, 03 Jun 2019 02:12:22: 4000000 INFO @ Mon, 03 Jun 2019 02:12:22: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:12:22: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:12:22: #1 total tags in treatment: 4143822 INFO @ Mon, 03 Jun 2019 02:12:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:12:22: #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 02:12:22: #1 tags after filtering in treatment: 4143822 INFO @ Mon, 03 Jun 2019 02:12:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:12:22: #1 finished! INFO @ Mon, 03 Jun 2019 02:12:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:12:23: #2 number of paired peaks: 176 WARNING @ Mon, 03 Jun 2019 02:12:23: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Mon, 03 Jun 2019 02:12:23: start model_add_line... INFO @ Mon, 03 Jun 2019 02:12:23: start X-correlation... INFO @ Mon, 03 Jun 2019 02:12:23: end of X-cor INFO @ Mon, 03 Jun 2019 02:12:23: #2 finished! INFO @ Mon, 03 Jun 2019 02:12:23: #2 predicted fragment length is 99 bps INFO @ Mon, 03 Jun 2019 02:12:23: #2 alternative fragment length(s) may be 4,85,99,540,562,578 bps INFO @ Mon, 03 Jun 2019 02:12:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.10_model.r WARNING @ Mon, 03 Jun 2019 02:12:23: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:12:23: #2 You may need to consider one of the other alternative d(s): 4,85,99,540,562,578 WARNING @ Mon, 03 Jun 2019 02:12:23: #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 02:12:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:12:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:12:23: 4000000 INFO @ Mon, 03 Jun 2019 02:12:24: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:12:24: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:12:24: #1 total tags in treatment: 4143822 INFO @ Mon, 03 Jun 2019 02:12:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:12:24: #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 02:12:24: #1 tags after filtering in treatment: 4143822 INFO @ Mon, 03 Jun 2019 02:12:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:12:24: #1 finished! INFO @ Mon, 03 Jun 2019 02:12:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:12:24: #2 number of paired peaks: 176 WARNING @ Mon, 03 Jun 2019 02:12:24: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Mon, 03 Jun 2019 02:12:24: start model_add_line... INFO @ Mon, 03 Jun 2019 02:12:24: start X-correlation... INFO @ Mon, 03 Jun 2019 02:12:24: end of X-cor INFO @ Mon, 03 Jun 2019 02:12:24: #2 finished! INFO @ Mon, 03 Jun 2019 02:12:24: #2 predicted fragment length is 99 bps INFO @ Mon, 03 Jun 2019 02:12:24: #2 alternative fragment length(s) may be 4,85,99,540,562,578 bps INFO @ Mon, 03 Jun 2019 02:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.05_model.r WARNING @ Mon, 03 Jun 2019 02:12:24: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:12:24: #2 You may need to consider one of the other alternative d(s): 4,85,99,540,562,578 WARNING @ Mon, 03 Jun 2019 02:12:24: #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 02:12:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:12:25: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:12:25: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:12:25: #1 total tags in treatment: 4143822 INFO @ Mon, 03 Jun 2019 02:12:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:12:25: #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 02:12:25: #1 tags after filtering in treatment: 4143822 INFO @ Mon, 03 Jun 2019 02:12:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:12:25: #1 finished! INFO @ Mon, 03 Jun 2019 02:12:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:12:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:12:25: #2 number of paired peaks: 176 WARNING @ Mon, 03 Jun 2019 02:12:25: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Mon, 03 Jun 2019 02:12:25: start model_add_line... INFO @ Mon, 03 Jun 2019 02:12:25: start X-correlation... INFO @ Mon, 03 Jun 2019 02:12:25: end of X-cor INFO @ Mon, 03 Jun 2019 02:12:25: #2 finished! INFO @ Mon, 03 Jun 2019 02:12:25: #2 predicted fragment length is 99 bps INFO @ Mon, 03 Jun 2019 02:12:25: #2 alternative fragment length(s) may be 4,85,99,540,562,578 bps INFO @ Mon, 03 Jun 2019 02:12:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.20_model.r WARNING @ Mon, 03 Jun 2019 02:12:25: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:12:25: #2 You may need to consider one of the other alternative d(s): 4,85,99,540,562,578 WARNING @ Mon, 03 Jun 2019 02:12:25: #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 02:12:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:12:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:12:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:12:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:12:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:12:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:12:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:12:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.10_summits.bed INFO @ Mon, 03 Jun 2019 02:12:41: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (60 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:12:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:12:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:12:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.05_summits.bed INFO @ Mon, 03 Jun 2019 02:12:44: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (117 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:12:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:12:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:12:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120694/SRX1120694.20_summits.bed INFO @ Mon, 03 Jun 2019 02:12:45: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。