Job ID = 1291796 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,511,216 reads read : 6,511,216 reads written : 6,511,216 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: 00:01:07 6511216 reads; of these: 6511216 (100.00%) were unpaired; of these: 201519 (3.09%) aligned 0 times 5320356 (81.71%) aligned exactly 1 time 989341 (15.19%) aligned >1 times 96.91% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 2834208 / 6309697 = 0.4492 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 16:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.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 16:31:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:31:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.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 16:31:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:31:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.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 16:31:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:31:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:31:54: 1000000 INFO @ Sun, 02 Jun 2019 16:31:55: 1000000 INFO @ Sun, 02 Jun 2019 16:31:56: 1000000 INFO @ Sun, 02 Jun 2019 16:32:00: 2000000 INFO @ Sun, 02 Jun 2019 16:32:01: 2000000 INFO @ Sun, 02 Jun 2019 16:32:04: 2000000 INFO @ Sun, 02 Jun 2019 16:32:06: 3000000 INFO @ Sun, 02 Jun 2019 16:32:08: 3000000 INFO @ Sun, 02 Jun 2019 16:32:09: #1 tag size is determined as 28 bps INFO @ Sun, 02 Jun 2019 16:32:09: #1 tag size = 28 INFO @ Sun, 02 Jun 2019 16:32:09: #1 total tags in treatment: 3475489 INFO @ Sun, 02 Jun 2019 16:32:09: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:32:09: #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 16:32:09: #1 tags after filtering in treatment: 3475489 INFO @ Sun, 02 Jun 2019 16:32:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:32:09: #1 finished! INFO @ Sun, 02 Jun 2019 16:32:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:32:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:32:10: #2 number of paired peaks: 788 WARNING @ Sun, 02 Jun 2019 16:32:10: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Sun, 02 Jun 2019 16:32:10: start model_add_line... INFO @ Sun, 02 Jun 2019 16:32:10: start X-correlation... INFO @ Sun, 02 Jun 2019 16:32:10: end of X-cor INFO @ Sun, 02 Jun 2019 16:32:10: #2 finished! INFO @ Sun, 02 Jun 2019 16:32:10: #2 predicted fragment length is 195 bps INFO @ Sun, 02 Jun 2019 16:32:10: #2 alternative fragment length(s) may be 195 bps INFO @ Sun, 02 Jun 2019 16:32:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.10_model.r INFO @ Sun, 02 Jun 2019 16:32:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:32:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:32:11: #1 tag size is determined as 28 bps INFO @ Sun, 02 Jun 2019 16:32:11: #1 tag size = 28 INFO @ Sun, 02 Jun 2019 16:32:11: #1 total tags in treatment: 3475489 INFO @ Sun, 02 Jun 2019 16:32:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:32:11: #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 16:32:12: #1 tags after filtering in treatment: 3475489 INFO @ Sun, 02 Jun 2019 16:32:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:32:12: #1 finished! INFO @ Sun, 02 Jun 2019 16:32:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:32:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:32:12: #2 number of paired peaks: 788 WARNING @ Sun, 02 Jun 2019 16:32:12: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Sun, 02 Jun 2019 16:32:12: start model_add_line... INFO @ Sun, 02 Jun 2019 16:32:12: start X-correlation... INFO @ Sun, 02 Jun 2019 16:32:12: 3000000 INFO @ Sun, 02 Jun 2019 16:32:12: end of X-cor INFO @ Sun, 02 Jun 2019 16:32:12: #2 finished! INFO @ Sun, 02 Jun 2019 16:32:12: #2 predicted fragment length is 195 bps INFO @ Sun, 02 Jun 2019 16:32:12: #2 alternative fragment length(s) may be 195 bps INFO @ Sun, 02 Jun 2019 16:32:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.05_model.r INFO @ Sun, 02 Jun 2019 16:32:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:32:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:32:16: #1 tag size is determined as 28 bps INFO @ Sun, 02 Jun 2019 16:32:16: #1 tag size = 28 INFO @ Sun, 02 Jun 2019 16:32:16: #1 total tags in treatment: 3475489 INFO @ Sun, 02 Jun 2019 16:32:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:32:16: #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 16:32:16: #1 tags after filtering in treatment: 3475489 INFO @ Sun, 02 Jun 2019 16:32:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:32:16: #1 finished! INFO @ Sun, 02 Jun 2019 16:32:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:32:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:32:17: #2 number of paired peaks: 788 WARNING @ Sun, 02 Jun 2019 16:32:17: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Sun, 02 Jun 2019 16:32:17: start model_add_line... INFO @ Sun, 02 Jun 2019 16:32:17: start X-correlation... INFO @ Sun, 02 Jun 2019 16:32:17: end of X-cor INFO @ Sun, 02 Jun 2019 16:32:17: #2 finished! INFO @ Sun, 02 Jun 2019 16:32:17: #2 predicted fragment length is 195 bps INFO @ Sun, 02 Jun 2019 16:32:17: #2 alternative fragment length(s) may be 195 bps INFO @ Sun, 02 Jun 2019 16:32:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.20_model.r INFO @ Sun, 02 Jun 2019 16:32:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:32:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:32:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:32:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:32:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:32:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:32:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.10_summits.bed INFO @ Sun, 02 Jun 2019 16:32:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (413 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:32:28: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:32:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:32:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:32:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.05_summits.bed INFO @ Sun, 02 Jun 2019 16:32:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (726 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:32:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:32:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:32:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257642/SRX257642.20_summits.bed INFO @ Sun, 02 Jun 2019 16:32:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (198 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。