Job ID = 1291811 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,762,765 reads read : 12,762,765 reads written : 12,762,765 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:04:20 12762765 reads; of these: 12762765 (100.00%) were unpaired; of these: 981756 (7.69%) aligned 0 times 9881249 (77.42%) aligned exactly 1 time 1899760 (14.89%) aligned >1 times 92.31% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 3868358 / 11781009 = 0.3284 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 @ Sun, 02 Jun 2019 16:37:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.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 @ Sun, 02 Jun 2019 16:37:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:37:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:37:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.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 @ Sun, 02 Jun 2019 16:37:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:37:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:37:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.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 @ Sun, 02 Jun 2019 16:37:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:37:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:37:57: 1000000 INFO @ Sun, 02 Jun 2019 16:37:58: 1000000 INFO @ Sun, 02 Jun 2019 16:37:58: 1000000 INFO @ Sun, 02 Jun 2019 16:38:10: 2000000 INFO @ Sun, 02 Jun 2019 16:38:10: 2000000 INFO @ Sun, 02 Jun 2019 16:38:11: 2000000 INFO @ Sun, 02 Jun 2019 16:38:23: 3000000 INFO @ Sun, 02 Jun 2019 16:38:24: 3000000 INFO @ Sun, 02 Jun 2019 16:38:24: 3000000 INFO @ Sun, 02 Jun 2019 16:38:36: 4000000 INFO @ Sun, 02 Jun 2019 16:38:38: 4000000 INFO @ Sun, 02 Jun 2019 16:38:38: 4000000 INFO @ Sun, 02 Jun 2019 16:38:50: 5000000 INFO @ Sun, 02 Jun 2019 16:38:51: 5000000 INFO @ Sun, 02 Jun 2019 16:38:51: 5000000 INFO @ Sun, 02 Jun 2019 16:39:04: 6000000 INFO @ Sun, 02 Jun 2019 16:39:05: 6000000 INFO @ Sun, 02 Jun 2019 16:39:05: 6000000 INFO @ Sun, 02 Jun 2019 16:39:18: 7000000 INFO @ Sun, 02 Jun 2019 16:39:18: 7000000 INFO @ Sun, 02 Jun 2019 16:39:19: 7000000 INFO @ Sun, 02 Jun 2019 16:39:30: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:39:30: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:39:30: #1 total tags in treatment: 7912651 INFO @ Sun, 02 Jun 2019 16:39:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:39:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:39:30: #1 tags after filtering in treatment: 7912651 INFO @ Sun, 02 Jun 2019 16:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:39:30: #1 finished! INFO @ Sun, 02 Jun 2019 16:39:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:39:30: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:39:30: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:39:30: #1 total tags in treatment: 7912651 INFO @ Sun, 02 Jun 2019 16:39:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:39:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:39:30: #1 tags after filtering in treatment: 7912651 INFO @ Sun, 02 Jun 2019 16:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:39:30: #1 finished! INFO @ Sun, 02 Jun 2019 16:39:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:39:31: #2 number of paired peaks: 529 WARNING @ Sun, 02 Jun 2019 16:39:31: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Sun, 02 Jun 2019 16:39:31: start model_add_line... INFO @ Sun, 02 Jun 2019 16:39:31: start X-correlation... INFO @ Sun, 02 Jun 2019 16:39:31: end of X-cor INFO @ Sun, 02 Jun 2019 16:39:31: #2 finished! INFO @ Sun, 02 Jun 2019 16:39:31: #2 predicted fragment length is 136 bps INFO @ Sun, 02 Jun 2019 16:39:31: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 02 Jun 2019 16:39:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.10_model.r INFO @ Sun, 02 Jun 2019 16:39:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:39:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:39:31: #2 number of paired peaks: 529 WARNING @ Sun, 02 Jun 2019 16:39:31: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Sun, 02 Jun 2019 16:39:31: start model_add_line... INFO @ Sun, 02 Jun 2019 16:39:31: start X-correlation... INFO @ Sun, 02 Jun 2019 16:39:31: end of X-cor INFO @ Sun, 02 Jun 2019 16:39:31: #2 finished! INFO @ Sun, 02 Jun 2019 16:39:31: #2 predicted fragment length is 136 bps INFO @ Sun, 02 Jun 2019 16:39:31: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 02 Jun 2019 16:39:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.20_model.r INFO @ Sun, 02 Jun 2019 16:39:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:39:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:39:32: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:39:32: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:39:32: #1 total tags in treatment: 7912651 INFO @ Sun, 02 Jun 2019 16:39:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:39:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:39:33: #1 tags after filtering in treatment: 7912651 INFO @ Sun, 02 Jun 2019 16:39:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:39:33: #1 finished! INFO @ Sun, 02 Jun 2019 16:39:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:39:34: #2 number of paired peaks: 529 WARNING @ Sun, 02 Jun 2019 16:39:34: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Sun, 02 Jun 2019 16:39:34: start model_add_line... INFO @ Sun, 02 Jun 2019 16:39:34: start X-correlation... INFO @ Sun, 02 Jun 2019 16:39:34: end of X-cor INFO @ Sun, 02 Jun 2019 16:39:34: #2 finished! INFO @ Sun, 02 Jun 2019 16:39:34: #2 predicted fragment length is 136 bps INFO @ Sun, 02 Jun 2019 16:39:34: #2 alternative fragment length(s) may be 136 bps INFO @ Sun, 02 Jun 2019 16:39:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.05_model.r INFO @ Sun, 02 Jun 2019 16:39:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:40:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:40:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:40:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:40:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:40:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:40:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.10_summits.bed INFO @ Sun, 02 Jun 2019 16:40:19: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (861 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:40:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:40:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:40:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.20_summits.bed INFO @ Sun, 02 Jun 2019 16:40:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (433 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:40:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:40:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:40:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257653/SRX257653.05_summits.bed INFO @ Sun, 02 Jun 2019 16:40:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1609 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。