Job ID = 2590221 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,392,700 reads read : 54,785,400 reads written : 27,392,700 reads 0-length : 27,392,700 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: 00:05:22 27392700 reads; of these: 27392700 (100.00%) were unpaired; of these: 7611721 (27.79%) aligned 0 times 16407192 (59.90%) aligned exactly 1 time 3373787 (12.32%) aligned >1 times 72.21% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9365806 / 19780979 = 0.4735 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 20:23:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.bam'] # control file = None # effective genome size = 9.00e+07 # 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 20:23:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:23:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:23:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.bam'] # control file = None # effective genome size = 9.00e+07 # 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 20:23:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:23:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.bam'] # control file = None # effective genome size = 9.00e+07 # 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 20:23:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:23:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:23:55: 1000000 INFO @ Mon, 12 Aug 2019 20:23:56: 1000000 INFO @ Mon, 12 Aug 2019 20:23:57: 1000000 INFO @ Mon, 12 Aug 2019 20:24:04: 2000000 INFO @ Mon, 12 Aug 2019 20:24:05: 2000000 INFO @ Mon, 12 Aug 2019 20:24:06: 2000000 INFO @ Mon, 12 Aug 2019 20:24:12: 3000000 INFO @ Mon, 12 Aug 2019 20:24:14: 3000000 INFO @ Mon, 12 Aug 2019 20:24:14: 3000000 INFO @ Mon, 12 Aug 2019 20:24:21: 4000000 INFO @ Mon, 12 Aug 2019 20:24:22: 4000000 INFO @ Mon, 12 Aug 2019 20:24:23: 4000000 INFO @ Mon, 12 Aug 2019 20:24:29: 5000000 INFO @ Mon, 12 Aug 2019 20:24:31: 5000000 INFO @ Mon, 12 Aug 2019 20:24:32: 5000000 INFO @ Mon, 12 Aug 2019 20:24:38: 6000000 INFO @ Mon, 12 Aug 2019 20:24:40: 6000000 INFO @ Mon, 12 Aug 2019 20:24:40: 6000000 INFO @ Mon, 12 Aug 2019 20:24:47: 7000000 INFO @ Mon, 12 Aug 2019 20:24:48: 7000000 INFO @ Mon, 12 Aug 2019 20:24:49: 7000000 INFO @ Mon, 12 Aug 2019 20:24:55: 8000000 INFO @ Mon, 12 Aug 2019 20:24:57: 8000000 INFO @ Mon, 12 Aug 2019 20:24:58: 8000000 INFO @ Mon, 12 Aug 2019 20:25:04: 9000000 INFO @ Mon, 12 Aug 2019 20:25:06: 9000000 INFO @ Mon, 12 Aug 2019 20:25:07: 9000000 INFO @ Mon, 12 Aug 2019 20:25:13: 10000000 INFO @ Mon, 12 Aug 2019 20:25:15: 10000000 INFO @ Mon, 12 Aug 2019 20:25:15: 10000000 INFO @ Mon, 12 Aug 2019 20:25:16: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:25:16: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:25:16: #1 total tags in treatment: 10415173 INFO @ Mon, 12 Aug 2019 20:25:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:25:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:25:16: #1 tags after filtering in treatment: 10415173 INFO @ Mon, 12 Aug 2019 20:25:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:25:16: #1 finished! INFO @ Mon, 12 Aug 2019 20:25:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:25:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:25:17: #2 number of paired peaks: 489 WARNING @ Mon, 12 Aug 2019 20:25:17: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Mon, 12 Aug 2019 20:25:17: start model_add_line... INFO @ Mon, 12 Aug 2019 20:25:17: start X-correlation... INFO @ Mon, 12 Aug 2019 20:25:17: end of X-cor INFO @ Mon, 12 Aug 2019 20:25:17: #2 finished! INFO @ Mon, 12 Aug 2019 20:25:17: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 20:25:17: #2 alternative fragment length(s) may be 1,43,527,550 bps INFO @ Mon, 12 Aug 2019 20:25:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.05_model.r WARNING @ Mon, 12 Aug 2019 20:25:17: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:25:17: #2 You may need to consider one of the other alternative d(s): 1,43,527,550 WARNING @ Mon, 12 Aug 2019 20:25:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:25:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:25:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:25:18: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:25:18: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:25:18: #1 total tags in treatment: 10415173 INFO @ Mon, 12 Aug 2019 20:25:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:25:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:25:18: #1 tags after filtering in treatment: 10415173 INFO @ Mon, 12 Aug 2019 20:25:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:25:18: #1 finished! INFO @ Mon, 12 Aug 2019 20:25:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:25:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:25:19: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:25:19: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:25:19: #1 total tags in treatment: 10415173 INFO @ Mon, 12 Aug 2019 20:25:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:25:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:25:19: #1 tags after filtering in treatment: 10415173 INFO @ Mon, 12 Aug 2019 20:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:25:19: #1 finished! INFO @ Mon, 12 Aug 2019 20:25:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:25:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:25:19: #2 number of paired peaks: 489 WARNING @ Mon, 12 Aug 2019 20:25:19: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Mon, 12 Aug 2019 20:25:19: start model_add_line... INFO @ Mon, 12 Aug 2019 20:25:20: start X-correlation... INFO @ Mon, 12 Aug 2019 20:25:20: end of X-cor INFO @ Mon, 12 Aug 2019 20:25:20: #2 finished! INFO @ Mon, 12 Aug 2019 20:25:20: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 20:25:20: #2 alternative fragment length(s) may be 1,43,527,550 bps INFO @ Mon, 12 Aug 2019 20:25:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.10_model.r WARNING @ Mon, 12 Aug 2019 20:25:20: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:25:20: #2 You may need to consider one of the other alternative d(s): 1,43,527,550 WARNING @ Mon, 12 Aug 2019 20:25:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:25:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:25:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:25:20: #2 number of paired peaks: 489 WARNING @ Mon, 12 Aug 2019 20:25:20: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Mon, 12 Aug 2019 20:25:20: start model_add_line... INFO @ Mon, 12 Aug 2019 20:25:20: start X-correlation... INFO @ Mon, 12 Aug 2019 20:25:20: end of X-cor INFO @ Mon, 12 Aug 2019 20:25:20: #2 finished! INFO @ Mon, 12 Aug 2019 20:25:20: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 20:25:20: #2 alternative fragment length(s) may be 1,43,527,550 bps INFO @ Mon, 12 Aug 2019 20:25:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.20_model.r WARNING @ Mon, 12 Aug 2019 20:25:20: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:25:20: #2 You may need to consider one of the other alternative d(s): 1,43,527,550 WARNING @ Mon, 12 Aug 2019 20:25:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:25:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:25:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:25:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:25:47: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:25:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:25:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:25:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:25:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.05_summits.bed INFO @ Mon, 12 Aug 2019 20:25:59: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (823 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:26:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:26:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:26:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.10_summits.bed INFO @ Mon, 12 Aug 2019 20:26:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (552 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:26:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:26:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:26:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709762/SRX5709762.20_summits.bed INFO @ Mon, 12 Aug 2019 20:26:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (218 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。