Job ID = 1306785 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,055,059 reads read : 6,055,059 reads written : 6,055,059 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: 00:02:24 6055059 reads; of these: 6055059 (100.00%) were unpaired; of these: 331056 (5.47%) aligned 0 times 3818066 (63.06%) aligned exactly 1 time 1905937 (31.48%) aligned >1 times 94.53% 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] 1428044 / 5724003 = 0.2495 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 22:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.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 22:01:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:01:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.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 22:01:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:01:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.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 22:01:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:01:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:01:41: 1000000 INFO @ Mon, 03 Jun 2019 22:01:42: 1000000 INFO @ Mon, 03 Jun 2019 22:01:44: 1000000 INFO @ Mon, 03 Jun 2019 22:01:49: 2000000 INFO @ Mon, 03 Jun 2019 22:01:51: 2000000 INFO @ Mon, 03 Jun 2019 22:01:54: 2000000 INFO @ Mon, 03 Jun 2019 22:01:57: 3000000 INFO @ Mon, 03 Jun 2019 22:02:00: 3000000 INFO @ Mon, 03 Jun 2019 22:02:04: 4000000 INFO @ Mon, 03 Jun 2019 22:02:05: 3000000 INFO @ Mon, 03 Jun 2019 22:02:06: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:02:06: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:02:06: #1 total tags in treatment: 4295959 INFO @ Mon, 03 Jun 2019 22:02:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:02:06: #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 22:02:06: #1 tags after filtering in treatment: 4295959 INFO @ Mon, 03 Jun 2019 22:02:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:02:06: #1 finished! INFO @ Mon, 03 Jun 2019 22:02:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:02:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:02:07: #2 number of paired peaks: 319 WARNING @ Mon, 03 Jun 2019 22:02:07: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Mon, 03 Jun 2019 22:02:07: start model_add_line... INFO @ Mon, 03 Jun 2019 22:02:07: start X-correlation... INFO @ Mon, 03 Jun 2019 22:02:07: end of X-cor INFO @ Mon, 03 Jun 2019 22:02:07: #2 finished! INFO @ Mon, 03 Jun 2019 22:02:07: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 22:02:07: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 22:02:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.05_model.r WARNING @ Mon, 03 Jun 2019 22:02:07: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:02:07: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 22:02:07: #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 22:02:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:02:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:02:08: 4000000 INFO @ Mon, 03 Jun 2019 22:02:10: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:02:10: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:02:10: #1 total tags in treatment: 4295959 INFO @ Mon, 03 Jun 2019 22:02:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:02:10: #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 22:02:10: #1 tags after filtering in treatment: 4295959 INFO @ Mon, 03 Jun 2019 22:02:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:02:10: #1 finished! INFO @ Mon, 03 Jun 2019 22:02:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:02:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:02:11: #2 number of paired peaks: 319 WARNING @ Mon, 03 Jun 2019 22:02:11: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Mon, 03 Jun 2019 22:02:11: start model_add_line... INFO @ Mon, 03 Jun 2019 22:02:11: start X-correlation... INFO @ Mon, 03 Jun 2019 22:02:11: end of X-cor INFO @ Mon, 03 Jun 2019 22:02:11: #2 finished! INFO @ Mon, 03 Jun 2019 22:02:11: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 22:02:11: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 22:02:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.20_model.r WARNING @ Mon, 03 Jun 2019 22:02:11: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:02:11: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 22:02:11: #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 22:02:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:02:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:02:14: 4000000 INFO @ Mon, 03 Jun 2019 22:02:17: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:02:17: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:02:17: #1 total tags in treatment: 4295959 INFO @ Mon, 03 Jun 2019 22:02:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:02:17: #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 22:02:17: #1 tags after filtering in treatment: 4295959 INFO @ Mon, 03 Jun 2019 22:02:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:02:17: #1 finished! INFO @ Mon, 03 Jun 2019 22:02:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:02:18: #2 number of paired peaks: 319 WARNING @ Mon, 03 Jun 2019 22:02:18: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Mon, 03 Jun 2019 22:02:18: start model_add_line... INFO @ Mon, 03 Jun 2019 22:02:18: start X-correlation... INFO @ Mon, 03 Jun 2019 22:02:18: end of X-cor INFO @ Mon, 03 Jun 2019 22:02:18: #2 finished! INFO @ Mon, 03 Jun 2019 22:02:18: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 22:02:18: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 22:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.10_model.r WARNING @ Mon, 03 Jun 2019 22:02:18: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:02:18: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 22:02:18: #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 22:02:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:02:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:02:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:02:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:02:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:02:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:02:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.05_summits.bed INFO @ Mon, 03 Jun 2019 22:02:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1037 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:02:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:02:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:02:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.20_summits.bed INFO @ Mon, 03 Jun 2019 22:02:30: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (215 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:02:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:02:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:02:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:02:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507388/SRX507388.10_summits.bed INFO @ Mon, 03 Jun 2019 22:02:37: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (639 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。