Job ID = 2589110 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,634,538 reads read : 9,634,538 reads written : 9,634,538 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: 00:02:44 9634538 reads; of these: 9634538 (100.00%) were unpaired; of these: 1629236 (16.91%) aligned 0 times 5479373 (56.87%) aligned exactly 1 time 2525929 (26.22%) aligned >1 times 83.09% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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_rmdupse_core] 2524539 / 8005302 = 0.3154 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 17:02:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.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 17:02:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:02:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:02:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.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 17:02:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:02:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:02:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.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 17:02:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:02:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:02:21: 1000000 INFO @ Mon, 12 Aug 2019 17:02:22: 1000000 INFO @ Mon, 12 Aug 2019 17:02:23: 1000000 INFO @ Mon, 12 Aug 2019 17:02:30: 2000000 INFO @ Mon, 12 Aug 2019 17:02:31: 2000000 INFO @ Mon, 12 Aug 2019 17:02:32: 2000000 INFO @ Mon, 12 Aug 2019 17:02:38: 3000000 INFO @ Mon, 12 Aug 2019 17:02:39: 3000000 INFO @ Mon, 12 Aug 2019 17:02:41: 3000000 INFO @ Mon, 12 Aug 2019 17:02:47: 4000000 INFO @ Mon, 12 Aug 2019 17:02:48: 4000000 INFO @ Mon, 12 Aug 2019 17:02:49: 4000000 INFO @ Mon, 12 Aug 2019 17:02:56: 5000000 INFO @ Mon, 12 Aug 2019 17:02:57: 5000000 INFO @ Mon, 12 Aug 2019 17:02:58: 5000000 INFO @ Mon, 12 Aug 2019 17:03:00: #1 tag size is determined as 48 bps INFO @ Mon, 12 Aug 2019 17:03:00: #1 tag size = 48 INFO @ Mon, 12 Aug 2019 17:03:00: #1 total tags in treatment: 5480763 INFO @ Mon, 12 Aug 2019 17:03:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:03:00: #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 17:03:00: #1 tags after filtering in treatment: 5480763 INFO @ Mon, 12 Aug 2019 17:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:03:00: #1 finished! INFO @ Mon, 12 Aug 2019 17:03:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:03:00: #2 number of paired peaks: 1140 INFO @ Mon, 12 Aug 2019 17:03:00: start model_add_line... INFO @ Mon, 12 Aug 2019 17:03:00: start X-correlation... INFO @ Mon, 12 Aug 2019 17:03:00: end of X-cor INFO @ Mon, 12 Aug 2019 17:03:00: #2 finished! INFO @ Mon, 12 Aug 2019 17:03:00: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 17:03:00: #2 alternative fragment length(s) may be 3,52,106 bps INFO @ Mon, 12 Aug 2019 17:03:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.05_model.r WARNING @ Mon, 12 Aug 2019 17:03:01: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:03:01: #2 You may need to consider one of the other alternative d(s): 3,52,106 WARNING @ Mon, 12 Aug 2019 17:03:01: #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 17:03:01: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:03:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:03:01: #1 tag size is determined as 48 bps INFO @ Mon, 12 Aug 2019 17:03:01: #1 tag size = 48 INFO @ Mon, 12 Aug 2019 17:03:01: #1 total tags in treatment: 5480763 INFO @ Mon, 12 Aug 2019 17:03:01: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:03:01: #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 17:03:01: #1 tags after filtering in treatment: 5480763 INFO @ Mon, 12 Aug 2019 17:03:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:03:01: #1 finished! INFO @ Mon, 12 Aug 2019 17:03:01: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:03:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:03:02: #2 number of paired peaks: 1140 INFO @ Mon, 12 Aug 2019 17:03:02: start model_add_line... INFO @ Mon, 12 Aug 2019 17:03:02: start X-correlation... INFO @ Mon, 12 Aug 2019 17:03:02: end of X-cor INFO @ Mon, 12 Aug 2019 17:03:02: #2 finished! INFO @ Mon, 12 Aug 2019 17:03:02: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 17:03:02: #2 alternative fragment length(s) may be 3,52,106 bps INFO @ Mon, 12 Aug 2019 17:03:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.10_model.r WARNING @ Mon, 12 Aug 2019 17:03:02: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:03:02: #2 You may need to consider one of the other alternative d(s): 3,52,106 WARNING @ Mon, 12 Aug 2019 17:03:02: #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 17:03:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:03:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:03:02: #1 tag size is determined as 48 bps INFO @ Mon, 12 Aug 2019 17:03:02: #1 tag size = 48 INFO @ Mon, 12 Aug 2019 17:03:02: #1 total tags in treatment: 5480763 INFO @ Mon, 12 Aug 2019 17:03:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:03:02: #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 17:03:02: #1 tags after filtering in treatment: 5480763 INFO @ Mon, 12 Aug 2019 17:03:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:03:02: #1 finished! INFO @ Mon, 12 Aug 2019 17:03:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:03:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:03:02: #2 number of paired peaks: 1140 INFO @ Mon, 12 Aug 2019 17:03:02: start model_add_line... INFO @ Mon, 12 Aug 2019 17:03:03: start X-correlation... INFO @ Mon, 12 Aug 2019 17:03:03: end of X-cor INFO @ Mon, 12 Aug 2019 17:03:03: #2 finished! INFO @ Mon, 12 Aug 2019 17:03:03: #2 predicted fragment length is 52 bps INFO @ Mon, 12 Aug 2019 17:03:03: #2 alternative fragment length(s) may be 3,52,106 bps INFO @ Mon, 12 Aug 2019 17:03:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.20_model.r WARNING @ Mon, 12 Aug 2019 17:03:03: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:03:03: #2 You may need to consider one of the other alternative d(s): 3,52,106 WARNING @ Mon, 12 Aug 2019 17:03:03: #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 17:03:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:03:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:03:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:03:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:03:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:03:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:03:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:03:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.05_summits.bed INFO @ Mon, 12 Aug 2019 17:03:24: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (473 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:03:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:03:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:03:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.10_summits.bed INFO @ Mon, 12 Aug 2019 17:03:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (236 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:03:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:03:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:03:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999212/ERX1999212.20_summits.bed INFO @ Mon, 12 Aug 2019 17:03:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (90 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。