Job ID = 2009004 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,526,863 reads read : 6,526,863 reads written : 6,526,863 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637572.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: 00:01:36 6526863 reads; of these: 6526863 (100.00%) were unpaired; of these: 2107904 (32.30%) aligned 0 times 2515018 (38.53%) aligned exactly 1 time 1903941 (29.17%) aligned >1 times 67.70% overall alignment rate Time searching: 00:01:36 Overall time: 00:01:36 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] 3202944 / 4418959 = 0.7248 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 19:10:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.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 19:10:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:10:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:10:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.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 19:10:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:10:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.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 19:10:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:10:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:10:59: 1000000 INFO @ Fri, 05 Jul 2019 19:11:00: 1000000 INFO @ Fri, 05 Jul 2019 19:11:01: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:11:01: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:11:01: #1 total tags in treatment: 1216015 INFO @ Fri, 05 Jul 2019 19:11:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:11:01: #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 19:11:01: #1 tags after filtering in treatment: 1216015 INFO @ Fri, 05 Jul 2019 19:11:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:11:01: #1 finished! INFO @ Fri, 05 Jul 2019 19:11:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:11:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:11:01: 1000000 INFO @ Fri, 05 Jul 2019 19:11:01: #2 number of paired peaks: 534 WARNING @ Fri, 05 Jul 2019 19:11:01: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Fri, 05 Jul 2019 19:11:01: start model_add_line... INFO @ Fri, 05 Jul 2019 19:11:01: start X-correlation... INFO @ Fri, 05 Jul 2019 19:11:01: end of X-cor INFO @ Fri, 05 Jul 2019 19:11:01: #2 finished! INFO @ Fri, 05 Jul 2019 19:11:01: #2 predicted fragment length is 155 bps INFO @ Fri, 05 Jul 2019 19:11:01: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 05 Jul 2019 19:11:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.05_model.r INFO @ Fri, 05 Jul 2019 19:11:01: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:11:01: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:11:01: #1 total tags in treatment: 1216015 INFO @ Fri, 05 Jul 2019 19:11:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:11:01: #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 19:11:01: #1 tags after filtering in treatment: 1216015 INFO @ Fri, 05 Jul 2019 19:11:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:11:01: #1 finished! INFO @ Fri, 05 Jul 2019 19:11:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:11:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:11:01: #2 number of paired peaks: 534 WARNING @ Fri, 05 Jul 2019 19:11:01: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Fri, 05 Jul 2019 19:11:01: start model_add_line... INFO @ Fri, 05 Jul 2019 19:11:01: start X-correlation... INFO @ Fri, 05 Jul 2019 19:11:01: end of X-cor INFO @ Fri, 05 Jul 2019 19:11:01: #2 finished! INFO @ Fri, 05 Jul 2019 19:11:01: #2 predicted fragment length is 155 bps INFO @ Fri, 05 Jul 2019 19:11:01: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 05 Jul 2019 19:11:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.10_model.r INFO @ Fri, 05 Jul 2019 19:11:02: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:11:02: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:11:02: #1 total tags in treatment: 1216015 INFO @ Fri, 05 Jul 2019 19:11:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:11:02: #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 19:11:02: #1 tags after filtering in treatment: 1216015 INFO @ Fri, 05 Jul 2019 19:11:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:11:02: #1 finished! INFO @ Fri, 05 Jul 2019 19:11:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:11:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:11:02: #2 number of paired peaks: 534 WARNING @ Fri, 05 Jul 2019 19:11:02: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Fri, 05 Jul 2019 19:11:02: start model_add_line... INFO @ Fri, 05 Jul 2019 19:11:02: start X-correlation... INFO @ Fri, 05 Jul 2019 19:11:02: end of X-cor INFO @ Fri, 05 Jul 2019 19:11:02: #2 finished! INFO @ Fri, 05 Jul 2019 19:11:02: #2 predicted fragment length is 155 bps INFO @ Fri, 05 Jul 2019 19:11:02: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 05 Jul 2019 19:11:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.20_model.r INFO @ Fri, 05 Jul 2019 19:11:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:11:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:11:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:11:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:11:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:11:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:11:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:11:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:11:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:11:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:11:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:11:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:11:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:11:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:11:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.20_summits.bed INFO @ Fri, 05 Jul 2019 19:11:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.10_summits.bed INFO @ Fri, 05 Jul 2019 19:11:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:11:15: Done! INFO @ Fri, 05 Jul 2019 19:11:15: Done! INFO @ Fri, 05 Jul 2019 19:11:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594022/ERX594022.05_summits.bed INFO @ Fri, 05 Jul 2019 19:11:15: Done! pass1 - making usageList (16 chroms): 1 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1283 records, 4 fields): 4 millis pass2 - checking and writing primary data (816 records, 4 fields): 5 millis pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1816 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling