Job ID = 2589105 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,535,468 reads read : 11,535,468 reads written : 11,535,468 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: 00:03:54 11535468 reads; of these: 11535468 (100.00%) were unpaired; of these: 693777 (6.01%) aligned 0 times 6059017 (52.53%) aligned exactly 1 time 4782674 (41.46%) aligned >1 times 93.99% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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 8 files... [bam_rmdupse_core] 5443693 / 10841691 = 0.5021 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 17:03:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.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 17:03:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:03:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:03:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.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 17:03:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:03:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:03:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.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 17:03:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:03:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:03:46: 1000000 INFO @ Mon, 12 Aug 2019 17:03:46: 1000000 INFO @ Mon, 12 Aug 2019 17:03:46: 1000000 INFO @ Mon, 12 Aug 2019 17:03:54: 2000000 INFO @ Mon, 12 Aug 2019 17:03:55: 2000000 INFO @ Mon, 12 Aug 2019 17:03:55: 2000000 INFO @ Mon, 12 Aug 2019 17:04:02: 3000000 INFO @ Mon, 12 Aug 2019 17:04:03: 3000000 INFO @ Mon, 12 Aug 2019 17:04:04: 3000000 INFO @ Mon, 12 Aug 2019 17:04:10: 4000000 INFO @ Mon, 12 Aug 2019 17:04:12: 4000000 INFO @ Mon, 12 Aug 2019 17:04:12: 4000000 INFO @ Mon, 12 Aug 2019 17:04:17: 5000000 INFO @ Mon, 12 Aug 2019 17:04:20: 5000000 INFO @ Mon, 12 Aug 2019 17:04:20: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 17:04:20: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 17:04:20: #1 total tags in treatment: 5397998 INFO @ Mon, 12 Aug 2019 17:04:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:04:20: #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 17:04:20: #1 tags after filtering in treatment: 5397998 INFO @ Mon, 12 Aug 2019 17:04:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:04:20: #1 finished! INFO @ Mon, 12 Aug 2019 17:04:20: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:04:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:04:21: 5000000 INFO @ Mon, 12 Aug 2019 17:04:21: #2 number of paired peaks: 4719 INFO @ Mon, 12 Aug 2019 17:04:21: start model_add_line... INFO @ Mon, 12 Aug 2019 17:04:21: start X-correlation... INFO @ Mon, 12 Aug 2019 17:04:21: end of X-cor INFO @ Mon, 12 Aug 2019 17:04:21: #2 finished! INFO @ Mon, 12 Aug 2019 17:04:21: #2 predicted fragment length is 3 bps INFO @ Mon, 12 Aug 2019 17:04:21: #2 alternative fragment length(s) may be 3,11,64,94,116 bps INFO @ Mon, 12 Aug 2019 17:04:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.20_model.r WARNING @ Mon, 12 Aug 2019 17:04:21: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:04:21: #2 You may need to consider one of the other alternative d(s): 3,11,64,94,116 WARNING @ Mon, 12 Aug 2019 17:04:21: #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 17:04:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:04:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:04:23: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 17:04:23: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 17:04:23: #1 total tags in treatment: 5397998 INFO @ Mon, 12 Aug 2019 17:04:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:04:23: #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 17:04:23: #1 tags after filtering in treatment: 5397998 INFO @ Mon, 12 Aug 2019 17:04:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:04:23: #1 finished! INFO @ Mon, 12 Aug 2019 17:04:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:04:24: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 17:04:24: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 17:04:24: #1 total tags in treatment: 5397998 INFO @ Mon, 12 Aug 2019 17:04:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:04:24: #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 17:04:24: #1 tags after filtering in treatment: 5397998 INFO @ Mon, 12 Aug 2019 17:04:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:04:24: #1 finished! INFO @ Mon, 12 Aug 2019 17:04:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:04:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:04:24: #2 number of paired peaks: 4719 INFO @ Mon, 12 Aug 2019 17:04:24: start model_add_line... INFO @ Mon, 12 Aug 2019 17:04:24: start X-correlation... INFO @ Mon, 12 Aug 2019 17:04:24: end of X-cor INFO @ Mon, 12 Aug 2019 17:04:24: #2 finished! INFO @ Mon, 12 Aug 2019 17:04:24: #2 predicted fragment length is 3 bps INFO @ Mon, 12 Aug 2019 17:04:24: #2 alternative fragment length(s) may be 3,11,64,94,116 bps INFO @ Mon, 12 Aug 2019 17:04:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.10_model.r WARNING @ Mon, 12 Aug 2019 17:04:24: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:04:24: #2 You may need to consider one of the other alternative d(s): 3,11,64,94,116 WARNING @ Mon, 12 Aug 2019 17:04:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:04:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:04:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:04:25: #2 number of paired peaks: 4719 INFO @ Mon, 12 Aug 2019 17:04:25: start model_add_line... INFO @ Mon, 12 Aug 2019 17:04:25: start X-correlation... INFO @ Mon, 12 Aug 2019 17:04:25: end of X-cor INFO @ Mon, 12 Aug 2019 17:04:25: #2 finished! INFO @ Mon, 12 Aug 2019 17:04:25: #2 predicted fragment length is 3 bps INFO @ Mon, 12 Aug 2019 17:04:25: #2 alternative fragment length(s) may be 3,11,64,94,116 bps INFO @ Mon, 12 Aug 2019 17:04:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.05_model.r WARNING @ Mon, 12 Aug 2019 17:04:25: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:04:25: #2 You may need to consider one of the other alternative d(s): 3,11,64,94,116 WARNING @ Mon, 12 Aug 2019 17:04:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:04:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:04:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:04:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:04:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:04:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:04:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:04:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:04:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.20_summits.bed INFO @ Mon, 12 Aug 2019 17:04:42: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:04:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:04:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:04:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.10_summits.bed INFO @ Mon, 12 Aug 2019 17:04:45: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:04:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:04:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:04:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999204/ERX1999204.05_summits.bed INFO @ Mon, 12 Aug 2019 17:04:46: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。