Job ID = 2008995 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,835,781 reads read : 7,835,781 reads written : 7,835,781 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637549.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: 00:01:17 7835781 reads; of these: 7835781 (100.00%) were unpaired; of these: 359927 (4.59%) aligned 0 times 6165339 (78.68%) aligned exactly 1 time 1310515 (16.72%) aligned >1 times 95.41% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 4362098 / 7475854 = 0.5835 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 19:03:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.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 19:03:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:03:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:03:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.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 19:03:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:03:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:03:18: 1000000 INFO @ Fri, 05 Jul 2019 19:03:19: 1000000 INFO @ Fri, 05 Jul 2019 19:03:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.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 19:03:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:03:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:03:26: 2000000 INFO @ Fri, 05 Jul 2019 19:03:28: 2000000 INFO @ Fri, 05 Jul 2019 19:03:29: 1000000 INFO @ Fri, 05 Jul 2019 19:03:34: 3000000 INFO @ Fri, 05 Jul 2019 19:03:34: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:03:34: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:03:34: #1 total tags in treatment: 3113756 INFO @ Fri, 05 Jul 2019 19:03:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:03:34: #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 19:03:35: #1 tags after filtering in treatment: 3113756 INFO @ Fri, 05 Jul 2019 19:03:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:03:35: #1 finished! INFO @ Fri, 05 Jul 2019 19:03:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:03:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:03:35: #2 number of paired peaks: 287 WARNING @ Fri, 05 Jul 2019 19:03:35: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Fri, 05 Jul 2019 19:03:35: start model_add_line... INFO @ Fri, 05 Jul 2019 19:03:35: start X-correlation... INFO @ Fri, 05 Jul 2019 19:03:35: end of X-cor INFO @ Fri, 05 Jul 2019 19:03:35: #2 finished! INFO @ Fri, 05 Jul 2019 19:03:35: #2 predicted fragment length is 115 bps INFO @ Fri, 05 Jul 2019 19:03:35: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 05 Jul 2019 19:03:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.10_model.r INFO @ Fri, 05 Jul 2019 19:03:36: 3000000 INFO @ Fri, 05 Jul 2019 19:03:37: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:03:37: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:03:37: #1 total tags in treatment: 3113756 INFO @ Fri, 05 Jul 2019 19:03:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:03:37: #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 19:03:37: #1 tags after filtering in treatment: 3113756 INFO @ Fri, 05 Jul 2019 19:03:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:03:37: #1 finished! INFO @ Fri, 05 Jul 2019 19:03:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:03:37: #2 number of paired peaks: 287 WARNING @ Fri, 05 Jul 2019 19:03:37: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Fri, 05 Jul 2019 19:03:37: start model_add_line... INFO @ Fri, 05 Jul 2019 19:03:37: start X-correlation... INFO @ Fri, 05 Jul 2019 19:03:37: end of X-cor INFO @ Fri, 05 Jul 2019 19:03:37: #2 finished! INFO @ Fri, 05 Jul 2019 19:03:37: #2 predicted fragment length is 115 bps INFO @ Fri, 05 Jul 2019 19:03:37: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 05 Jul 2019 19:03:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.05_model.r INFO @ Fri, 05 Jul 2019 19:03:38: 2000000 INFO @ Fri, 05 Jul 2019 19:03:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:03:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:03:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:03:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:03:46: 3000000 INFO @ Fri, 05 Jul 2019 19:03:47: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:03:47: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:03:47: #1 total tags in treatment: 3113756 INFO @ Fri, 05 Jul 2019 19:03:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:03:47: #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 19:03:47: #1 tags after filtering in treatment: 3113756 INFO @ Fri, 05 Jul 2019 19:03:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:03:47: #1 finished! INFO @ Fri, 05 Jul 2019 19:03:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:03:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:03:47: #2 number of paired peaks: 287 WARNING @ Fri, 05 Jul 2019 19:03:47: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Fri, 05 Jul 2019 19:03:47: start model_add_line... INFO @ Fri, 05 Jul 2019 19:03:47: start X-correlation... INFO @ Fri, 05 Jul 2019 19:03:47: end of X-cor INFO @ Fri, 05 Jul 2019 19:03:47: #2 finished! INFO @ Fri, 05 Jul 2019 19:03:47: #2 predicted fragment length is 115 bps INFO @ Fri, 05 Jul 2019 19:03:47: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 05 Jul 2019 19:03:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.20_model.r INFO @ Fri, 05 Jul 2019 19:03:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:03:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:03:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:03:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:03:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:03:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.05_peaks.xls BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 19:03:58: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:04:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.20_peaks.xls BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:04:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:04:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:04:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.20_summits.bed INFO @ Fri, 05 Jul 2019 19:04:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:04:10: Done! INFO @ Fri, 05 Jul 2019 19:04:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.10_summits.bed INFO @ Fri, 05 Jul 2019 19:04:10: Done! INFO @ Fri, 05 Jul 2019 19:04:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594015/ERX594015.05_summits.bed INFO @ Fri, 05 Jul 2019 19:04:10: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (2871 records, 4 fields): 12 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (4398 records, 4 fields): 7 millis pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (5693 records, 4 fields): 8 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。