Job ID = 1292839 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: 00:03:00 12762765 reads; of these: 12762765 (100.00%) were unpaired; of these: 981756 (7.69%) aligned 0 times 9881166 (77.42%) aligned exactly 1 time 1899843 (14.89%) aligned >1 times 92.31% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 3868437 / 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 20:57:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.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 20:57:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:57:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:57:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.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 20:57:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:57:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:57:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.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 20:57:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:57:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:57:11: 1000000 INFO @ Sun, 02 Jun 2019 20:57:12: 1000000 INFO @ Sun, 02 Jun 2019 20:57:12: 1000000 INFO @ Sun, 02 Jun 2019 20:57:18: 2000000 INFO @ Sun, 02 Jun 2019 20:57:19: 2000000 INFO @ Sun, 02 Jun 2019 20:57:20: 2000000 INFO @ Sun, 02 Jun 2019 20:57:26: 3000000 INFO @ Sun, 02 Jun 2019 20:57:26: 3000000 INFO @ Sun, 02 Jun 2019 20:57:28: 3000000 INFO @ Sun, 02 Jun 2019 20:57:33: 4000000 INFO @ Sun, 02 Jun 2019 20:57:33: 4000000 INFO @ Sun, 02 Jun 2019 20:57:36: 4000000 INFO @ Sun, 02 Jun 2019 20:57:40: 5000000 INFO @ Sun, 02 Jun 2019 20:57:40: 5000000 INFO @ Sun, 02 Jun 2019 20:57:44: 5000000 INFO @ Sun, 02 Jun 2019 20:57:47: 6000000 INFO @ Sun, 02 Jun 2019 20:57:47: 6000000 INFO @ Sun, 02 Jun 2019 20:57:52: 6000000 INFO @ Sun, 02 Jun 2019 20:57:54: 7000000 INFO @ Sun, 02 Jun 2019 20:57:54: 7000000 INFO @ Sun, 02 Jun 2019 20:57:59: 7000000 INFO @ Sun, 02 Jun 2019 20:58:00: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:58:00: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:58:00: #1 total tags in treatment: 7912572 INFO @ Sun, 02 Jun 2019 20:58:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:58:00: #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 20:58:00: #1 tags after filtering in treatment: 7912572 INFO @ Sun, 02 Jun 2019 20:58:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:58:00: #1 finished! INFO @ Sun, 02 Jun 2019 20:58:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:58:00: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:58:00: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:58:00: #1 total tags in treatment: 7912572 INFO @ Sun, 02 Jun 2019 20:58:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:58:00: #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 20:58:01: #1 tags after filtering in treatment: 7912572 INFO @ Sun, 02 Jun 2019 20:58:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:58:01: #1 finished! INFO @ Sun, 02 Jun 2019 20:58:01: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:58:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:58:01: #2 number of paired peaks: 540 WARNING @ Sun, 02 Jun 2019 20:58:01: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Sun, 02 Jun 2019 20:58:01: start model_add_line... INFO @ Sun, 02 Jun 2019 20:58:01: start X-correlation... INFO @ Sun, 02 Jun 2019 20:58:01: end of X-cor INFO @ Sun, 02 Jun 2019 20:58:01: #2 finished! INFO @ Sun, 02 Jun 2019 20:58:01: #2 predicted fragment length is 127 bps INFO @ Sun, 02 Jun 2019 20:58:01: #2 alternative fragment length(s) may be 127 bps INFO @ Sun, 02 Jun 2019 20:58:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.20_model.r INFO @ Sun, 02 Jun 2019 20:58:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:58:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:58:01: #2 number of paired peaks: 540 WARNING @ Sun, 02 Jun 2019 20:58:01: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Sun, 02 Jun 2019 20:58:01: start model_add_line... INFO @ Sun, 02 Jun 2019 20:58:01: start X-correlation... INFO @ Sun, 02 Jun 2019 20:58:01: end of X-cor INFO @ Sun, 02 Jun 2019 20:58:01: #2 finished! INFO @ Sun, 02 Jun 2019 20:58:01: #2 predicted fragment length is 127 bps INFO @ Sun, 02 Jun 2019 20:58:01: #2 alternative fragment length(s) may be 127 bps INFO @ Sun, 02 Jun 2019 20:58:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.10_model.r INFO @ Sun, 02 Jun 2019 20:58:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:58:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:58:06: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:58:06: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:58:06: #1 total tags in treatment: 7912572 INFO @ Sun, 02 Jun 2019 20:58:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:58:06: #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 20:58:06: #1 tags after filtering in treatment: 7912572 INFO @ Sun, 02 Jun 2019 20:58:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:58:06: #1 finished! INFO @ Sun, 02 Jun 2019 20:58:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:58:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:58:07: #2 number of paired peaks: 540 WARNING @ Sun, 02 Jun 2019 20:58:07: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Sun, 02 Jun 2019 20:58:07: start model_add_line... INFO @ Sun, 02 Jun 2019 20:58:07: start X-correlation... INFO @ Sun, 02 Jun 2019 20:58:07: end of X-cor INFO @ Sun, 02 Jun 2019 20:58:07: #2 finished! INFO @ Sun, 02 Jun 2019 20:58:07: #2 predicted fragment length is 127 bps INFO @ Sun, 02 Jun 2019 20:58:07: #2 alternative fragment length(s) may be 127 bps INFO @ Sun, 02 Jun 2019 20:58:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.05_model.r INFO @ Sun, 02 Jun 2019 20:58:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:58:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:58:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:58:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:58:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.20_summits.bed INFO @ Sun, 02 Jun 2019 20:58:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (412 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.10_summits.bed INFO @ Sun, 02 Jun 2019 20:58:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (857 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:58:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:58:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:58:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495075/SRX495075.05_summits.bed INFO @ Sun, 02 Jun 2019 20:58:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1562 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。