Job ID = 2590866 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,094,542 reads read : 32,189,084 reads written : 16,094,542 reads 0-length : 16,094,542 rm: cannot remove ‘[DSE]RR*’: 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: 00:06:27 16094542 reads; of these: 16094542 (100.00%) were unpaired; of these: 2512222 (15.61%) aligned 0 times 10539156 (65.48%) aligned exactly 1 time 3043164 (18.91%) aligned >1 times 84.39% overall alignment rate Time searching: 00:06:27 Overall time: 00:06:27 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] 3190123 / 13582320 = 0.2349 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, 12 Aug 2019 23:59:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.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, 12 Aug 2019 23:59:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:59:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:59:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.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, 12 Aug 2019 23:59:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:59:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:59:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.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, 12 Aug 2019 23:59:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:59:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:59:24: 1000000 INFO @ Mon, 12 Aug 2019 23:59:25: 1000000 INFO @ Mon, 12 Aug 2019 23:59:26: 1000000 INFO @ Mon, 12 Aug 2019 23:59:32: 2000000 INFO @ Mon, 12 Aug 2019 23:59:33: 2000000 INFO @ Mon, 12 Aug 2019 23:59:36: 2000000 INFO @ Mon, 12 Aug 2019 23:59:40: 3000000 INFO @ Mon, 12 Aug 2019 23:59:41: 3000000 INFO @ Mon, 12 Aug 2019 23:59:47: 3000000 INFO @ Mon, 12 Aug 2019 23:59:48: 4000000 INFO @ Mon, 12 Aug 2019 23:59:49: 4000000 INFO @ Mon, 12 Aug 2019 23:59:56: 5000000 INFO @ Mon, 12 Aug 2019 23:59:57: 5000000 INFO @ Mon, 12 Aug 2019 23:59:57: 4000000 INFO @ Tue, 13 Aug 2019 00:00:03: 6000000 INFO @ Tue, 13 Aug 2019 00:00:05: 6000000 INFO @ Tue, 13 Aug 2019 00:00:08: 5000000 INFO @ Tue, 13 Aug 2019 00:00:11: 7000000 INFO @ Tue, 13 Aug 2019 00:00:12: 7000000 INFO @ Tue, 13 Aug 2019 00:00:18: 6000000 INFO @ Tue, 13 Aug 2019 00:00:19: 8000000 INFO @ Tue, 13 Aug 2019 00:00:20: 8000000 INFO @ Tue, 13 Aug 2019 00:00:26: 9000000 INFO @ Tue, 13 Aug 2019 00:00:27: 9000000 INFO @ Tue, 13 Aug 2019 00:00:28: 7000000 INFO @ Tue, 13 Aug 2019 00:00:34: 10000000 INFO @ Tue, 13 Aug 2019 00:00:35: 10000000 INFO @ Tue, 13 Aug 2019 00:00:37: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:00:37: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:00:37: #1 total tags in treatment: 10392197 INFO @ Tue, 13 Aug 2019 00:00:37: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:00:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:00:37: #1 tags after filtering in treatment: 10392197 INFO @ Tue, 13 Aug 2019 00:00:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:00:37: #1 finished! INFO @ Tue, 13 Aug 2019 00:00:37: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:00:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:00:38: 8000000 INFO @ Tue, 13 Aug 2019 00:00:38: #2 number of paired peaks: 945 WARNING @ Tue, 13 Aug 2019 00:00:38: Fewer paired peaks (945) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 945 pairs to build model! INFO @ Tue, 13 Aug 2019 00:00:38: start model_add_line... INFO @ Tue, 13 Aug 2019 00:00:38: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:00:38: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:00:38: #1 total tags in treatment: 10392197 INFO @ Tue, 13 Aug 2019 00:00:38: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:00:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:00:38: start X-correlation... INFO @ Tue, 13 Aug 2019 00:00:38: end of X-cor INFO @ Tue, 13 Aug 2019 00:00:38: #2 finished! INFO @ Tue, 13 Aug 2019 00:00:38: #2 predicted fragment length is 108 bps INFO @ Tue, 13 Aug 2019 00:00:38: #2 alternative fragment length(s) may be 108 bps INFO @ Tue, 13 Aug 2019 00:00:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.10_model.r WARNING @ Tue, 13 Aug 2019 00:00:38: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:00:38: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Tue, 13 Aug 2019 00:00:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:00:38: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:00:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:00:38: #1 tags after filtering in treatment: 10392197 INFO @ Tue, 13 Aug 2019 00:00:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:00:38: #1 finished! INFO @ Tue, 13 Aug 2019 00:00:38: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:00:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:00:39: #2 number of paired peaks: 945 WARNING @ Tue, 13 Aug 2019 00:00:39: Fewer paired peaks (945) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 945 pairs to build model! INFO @ Tue, 13 Aug 2019 00:00:39: start model_add_line... INFO @ Tue, 13 Aug 2019 00:00:39: start X-correlation... INFO @ Tue, 13 Aug 2019 00:00:39: end of X-cor INFO @ Tue, 13 Aug 2019 00:00:39: #2 finished! INFO @ Tue, 13 Aug 2019 00:00:39: #2 predicted fragment length is 108 bps INFO @ Tue, 13 Aug 2019 00:00:39: #2 alternative fragment length(s) may be 108 bps INFO @ Tue, 13 Aug 2019 00:00:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.20_model.r WARNING @ Tue, 13 Aug 2019 00:00:39: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:00:39: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Tue, 13 Aug 2019 00:00:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:00:39: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:00:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:00:47: 9000000 INFO @ Tue, 13 Aug 2019 00:00:57: 10000000 INFO @ Tue, 13 Aug 2019 00:01:01: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:01:01: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:01:01: #1 total tags in treatment: 10392197 INFO @ Tue, 13 Aug 2019 00:01:01: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:01:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:01:01: #1 tags after filtering in treatment: 10392197 INFO @ Tue, 13 Aug 2019 00:01:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:01:01: #1 finished! INFO @ Tue, 13 Aug 2019 00:01:01: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:01:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:01:02: #2 number of paired peaks: 945 WARNING @ Tue, 13 Aug 2019 00:01:02: Fewer paired peaks (945) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 945 pairs to build model! INFO @ Tue, 13 Aug 2019 00:01:02: start model_add_line... INFO @ Tue, 13 Aug 2019 00:01:02: start X-correlation... INFO @ Tue, 13 Aug 2019 00:01:02: end of X-cor INFO @ Tue, 13 Aug 2019 00:01:02: #2 finished! INFO @ Tue, 13 Aug 2019 00:01:02: #2 predicted fragment length is 108 bps INFO @ Tue, 13 Aug 2019 00:01:02: #2 alternative fragment length(s) may be 108 bps INFO @ Tue, 13 Aug 2019 00:01:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.05_model.r WARNING @ Tue, 13 Aug 2019 00:01:02: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:01:02: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Tue, 13 Aug 2019 00:01:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:01:02: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:01:09: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:01:10: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:01:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:01:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:01:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.10_summits.bed INFO @ Tue, 13 Aug 2019 00:01:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1822 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:01:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:01:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:01:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.20_summits.bed INFO @ Tue, 13 Aug 2019 00:01:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (866 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:01:33: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:01:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:01:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:01:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5053150/SRX5053150.05_summits.bed INFO @ Tue, 13 Aug 2019 00:01:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3456 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。