Job ID = 2589367 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,112,029 reads read : 23,112,029 reads written : 23,112,029 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:14 23112029 reads; of these: 23112029 (100.00%) were unpaired; of these: 10693824 (46.27%) aligned 0 times 10307801 (44.60%) aligned exactly 1 time 2110404 (9.13%) aligned >1 times 53.73% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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] 10581840 / 12418205 = 0.8521 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 17:50:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.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 17:50:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:50:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:50:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.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 17:50:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:50:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.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 17:50:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:50:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:50:25: 1000000 INFO @ Mon, 12 Aug 2019 17:50:27: 1000000 INFO @ Mon, 12 Aug 2019 17:50:28: 1000000 INFO @ Mon, 12 Aug 2019 17:50:33: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:50:33: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:50:33: #1 total tags in treatment: 1836365 INFO @ Mon, 12 Aug 2019 17:50:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:50:33: #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 17:50:33: #1 tags after filtering in treatment: 1836365 INFO @ Mon, 12 Aug 2019 17:50:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:50:33: #1 finished! INFO @ Mon, 12 Aug 2019 17:50:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:50:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:50:33: #2 number of paired peaks: 1030 INFO @ Mon, 12 Aug 2019 17:50:33: start model_add_line... INFO @ Mon, 12 Aug 2019 17:50:33: start X-correlation... INFO @ Mon, 12 Aug 2019 17:50:33: end of X-cor INFO @ Mon, 12 Aug 2019 17:50:33: #2 finished! INFO @ Mon, 12 Aug 2019 17:50:33: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 17:50:33: #2 alternative fragment length(s) may be 50,544,561 bps INFO @ Mon, 12 Aug 2019 17:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.05_model.r WARNING @ Mon, 12 Aug 2019 17:50:34: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:50:34: #2 You may need to consider one of the other alternative d(s): 50,544,561 WARNING @ Mon, 12 Aug 2019 17:50:34: #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 17:50:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:50:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:50:36: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:50:36: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:50:36: #1 total tags in treatment: 1836365 INFO @ Mon, 12 Aug 2019 17:50:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:50:36: #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 17:50:36: #1 tags after filtering in treatment: 1836365 INFO @ Mon, 12 Aug 2019 17:50:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:50:36: #1 finished! INFO @ Mon, 12 Aug 2019 17:50:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:50:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:50:37: #2 number of paired peaks: 1030 INFO @ Mon, 12 Aug 2019 17:50:37: start model_add_line... INFO @ Mon, 12 Aug 2019 17:50:37: start X-correlation... INFO @ Mon, 12 Aug 2019 17:50:37: end of X-cor INFO @ Mon, 12 Aug 2019 17:50:37: #2 finished! INFO @ Mon, 12 Aug 2019 17:50:37: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 17:50:37: #2 alternative fragment length(s) may be 50,544,561 bps INFO @ Mon, 12 Aug 2019 17:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.10_model.r WARNING @ Mon, 12 Aug 2019 17:50:37: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:50:37: #2 You may need to consider one of the other alternative d(s): 50,544,561 WARNING @ Mon, 12 Aug 2019 17:50:37: #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 17:50:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:50:37: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 17:50:37: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 17:50:37: #1 total tags in treatment: 1836365 INFO @ Mon, 12 Aug 2019 17:50:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:50:37: #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 17:50:38: #1 tags after filtering in treatment: 1836365 INFO @ Mon, 12 Aug 2019 17:50:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:50:38: #1 finished! INFO @ Mon, 12 Aug 2019 17:50:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:50:38: #2 number of paired peaks: 1030 INFO @ Mon, 12 Aug 2019 17:50:38: start model_add_line... INFO @ Mon, 12 Aug 2019 17:50:38: start X-correlation... INFO @ Mon, 12 Aug 2019 17:50:38: end of X-cor INFO @ Mon, 12 Aug 2019 17:50:38: #2 finished! INFO @ Mon, 12 Aug 2019 17:50:38: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 17:50:38: #2 alternative fragment length(s) may be 50,544,561 bps INFO @ Mon, 12 Aug 2019 17:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.20_model.r WARNING @ Mon, 12 Aug 2019 17:50:38: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:50:38: #2 You may need to consider one of the other alternative d(s): 50,544,561 WARNING @ Mon, 12 Aug 2019 17:50:38: #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 17:50:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:50:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:50:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:50:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:50:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:50:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.05_summits.bed INFO @ Mon, 12 Aug 2019 17:50:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (748 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:50:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:50:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:50:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:50:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:50:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.10_summits.bed INFO @ Mon, 12 Aug 2019 17:50:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (529 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:50:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:50:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:50:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078719/SRX1078719.20_summits.bed INFO @ Mon, 12 Aug 2019 17:50:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (248 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。