Job ID = 2009007 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,092,368 reads read : 4,092,368 reads written : 4,092,368 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637576.sra.cache’: 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: 00:00:42 4092368 reads; of these: 4092368 (100.00%) were unpaired; of these: 507937 (12.41%) aligned 0 times 2328114 (56.89%) aligned exactly 1 time 1256317 (30.70%) aligned >1 times 87.59% overall alignment rate Time searching: 00:00:42 Overall time: 00:00:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 2362987 / 3584431 = 0.6592 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 @ Fri, 05 Jul 2019 19:06:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 19:06:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:06:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:06:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 19:06:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:06:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:06:11: 1000000 INFO @ Fri, 05 Jul 2019 19:06:12: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:06:12: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:06:12: #1 total tags in treatment: 1221444 INFO @ Fri, 05 Jul 2019 19:06:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:06:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:06:12: #1 tags after filtering in treatment: 1221444 INFO @ Fri, 05 Jul 2019 19:06:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:06:12: #1 finished! INFO @ Fri, 05 Jul 2019 19:06:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:06:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:06:13: #2 number of paired peaks: 444 WARNING @ Fri, 05 Jul 2019 19:06:13: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Fri, 05 Jul 2019 19:06:13: start model_add_line... INFO @ Fri, 05 Jul 2019 19:06:13: start X-correlation... INFO @ Fri, 05 Jul 2019 19:06:13: end of X-cor INFO @ Fri, 05 Jul 2019 19:06:13: #2 finished! INFO @ Fri, 05 Jul 2019 19:06:13: #2 predicted fragment length is 167 bps INFO @ Fri, 05 Jul 2019 19:06:13: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 05 Jul 2019 19:06:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.05_model.r INFO @ Fri, 05 Jul 2019 19:06:14: 1000000 INFO @ Fri, 05 Jul 2019 19:06:16: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:06:16: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:06:16: #1 total tags in treatment: 1221444 INFO @ Fri, 05 Jul 2019 19:06:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:06:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:06:16: #1 tags after filtering in treatment: 1221444 INFO @ Fri, 05 Jul 2019 19:06:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:06:16: #1 finished! INFO @ Fri, 05 Jul 2019 19:06:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:06:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:06:16: #2 number of paired peaks: 444 WARNING @ Fri, 05 Jul 2019 19:06:16: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Fri, 05 Jul 2019 19:06:16: start model_add_line... INFO @ Fri, 05 Jul 2019 19:06:16: start X-correlation... INFO @ Fri, 05 Jul 2019 19:06:16: end of X-cor INFO @ Fri, 05 Jul 2019 19:06:16: #2 finished! INFO @ Fri, 05 Jul 2019 19:06:16: #2 predicted fragment length is 167 bps INFO @ Fri, 05 Jul 2019 19:06:16: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 05 Jul 2019 19:06:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.10_model.r INFO @ Fri, 05 Jul 2019 19:06:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:06:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:06:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:06:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:06:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 05 Jul 2019 19:06:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:06:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:06:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:06:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.05_summits.bed INFO @ Fri, 05 Jul 2019 19:06:41: Done! INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.10_peaks.narrowPeak pass1 - making usageList (16 chroms): 1 millis INFO @ Fri, 05 Jul 2019 19:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.10_summits.bed pass2 - checking and writing primary data (1941 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 19:06:41: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1318 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 19:06:45: 1000000 CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:06:46: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:06:46: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:06:46: #1 total tags in treatment: 1221444 INFO @ Fri, 05 Jul 2019 19:06:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:06:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:06:46: #1 tags after filtering in treatment: 1221444 INFO @ Fri, 05 Jul 2019 19:06:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:06:46: #1 finished! INFO @ Fri, 05 Jul 2019 19:06:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:06:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:06:46: #2 number of paired peaks: 444 WARNING @ Fri, 05 Jul 2019 19:06:46: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Fri, 05 Jul 2019 19:06:46: start model_add_line... INFO @ Fri, 05 Jul 2019 19:06:46: start X-correlation... INFO @ Fri, 05 Jul 2019 19:06:46: end of X-cor INFO @ Fri, 05 Jul 2019 19:06:46: #2 finished! INFO @ Fri, 05 Jul 2019 19:06:46: #2 predicted fragment length is 167 bps INFO @ Fri, 05 Jul 2019 19:06:46: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 05 Jul 2019 19:06:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.20_model.r INFO @ Fri, 05 Jul 2019 19:06:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:06:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:06:51: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:06:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.20_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:07:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:07:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594025/ERX594025.20_summits.bed INFO @ Fri, 05 Jul 2019 19:07:31: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (846 records, 4 fields): 6 millis BigWig に変換しました。 CompletedMACS2peakCalling