Job ID = 2008379 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,563,299 reads read : 8,563,299 reads written : 8,563,299 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637604.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: 00:02:23 8563299 reads; of these: 8563299 (100.00%) were unpaired; of these: 2613272 (30.52%) aligned 0 times 3277528 (38.27%) aligned exactly 1 time 2672499 (31.21%) aligned >1 times 69.48% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 4424567 / 5950027 = 0.7436 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 18:56:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.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 18:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.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 18:56:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:57:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.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 18:57:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:57:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:57:06: 1000000 INFO @ Fri, 05 Jul 2019 18:57:06: 1000000 INFO @ Fri, 05 Jul 2019 18:57:09: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:57:09: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:57:09: #1 total tags in treatment: 1525460 INFO @ Fri, 05 Jul 2019 18:57:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:57:09: #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 18:57:10: #1 tags after filtering in treatment: 1525460 INFO @ Fri, 05 Jul 2019 18:57:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:57:10: #1 finished! INFO @ Fri, 05 Jul 2019 18:57:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:57:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:57:10: #2 number of paired peaks: 503 WARNING @ Fri, 05 Jul 2019 18:57:10: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Fri, 05 Jul 2019 18:57:10: start model_add_line... INFO @ Fri, 05 Jul 2019 18:57:10: start X-correlation... INFO @ Fri, 05 Jul 2019 18:57:10: 1000000 INFO @ Fri, 05 Jul 2019 18:57:10: end of X-cor INFO @ Fri, 05 Jul 2019 18:57:10: #2 finished! INFO @ Fri, 05 Jul 2019 18:57:10: #2 predicted fragment length is 159 bps INFO @ Fri, 05 Jul 2019 18:57:10: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 05 Jul 2019 18:57:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.05_model.r INFO @ Fri, 05 Jul 2019 18:57:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:57:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:57:11: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:57:11: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:57:11: #1 total tags in treatment: 1525460 INFO @ Fri, 05 Jul 2019 18:57:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:57:11: #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 18:57:11: #1 tags after filtering in treatment: 1525460 INFO @ Fri, 05 Jul 2019 18:57:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:57:11: #1 finished! INFO @ Fri, 05 Jul 2019 18:57:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:57:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:57:11: #2 number of paired peaks: 503 WARNING @ Fri, 05 Jul 2019 18:57:11: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Fri, 05 Jul 2019 18:57:11: start model_add_line... INFO @ Fri, 05 Jul 2019 18:57:11: start X-correlation... INFO @ Fri, 05 Jul 2019 18:57:11: end of X-cor INFO @ Fri, 05 Jul 2019 18:57:11: #2 finished! INFO @ Fri, 05 Jul 2019 18:57:11: #2 predicted fragment length is 159 bps INFO @ Fri, 05 Jul 2019 18:57:11: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 05 Jul 2019 18:57:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.10_model.r INFO @ Fri, 05 Jul 2019 18:57:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:57:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:57:14: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:57:14: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:57:14: #1 total tags in treatment: 1525460 INFO @ Fri, 05 Jul 2019 18:57:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:57:14: #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 18:57:14: #1 tags after filtering in treatment: 1525460 INFO @ Fri, 05 Jul 2019 18:57:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:57:14: #1 finished! INFO @ Fri, 05 Jul 2019 18:57:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:57:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:57:14: #2 number of paired peaks: 503 WARNING @ Fri, 05 Jul 2019 18:57:14: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Fri, 05 Jul 2019 18:57:14: start model_add_line... INFO @ Fri, 05 Jul 2019 18:57:14: start X-correlation... INFO @ Fri, 05 Jul 2019 18:57:14: end of X-cor INFO @ Fri, 05 Jul 2019 18:57:14: #2 finished! INFO @ Fri, 05 Jul 2019 18:57:14: #2 predicted fragment length is 159 bps INFO @ Fri, 05 Jul 2019 18:57:14: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 05 Jul 2019 18:57:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.20_model.r INFO @ Fri, 05 Jul 2019 18:57:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:57:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:57:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:57:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.10_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:57:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:57:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:57:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:57:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:57:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.10_summits.bed INFO @ Fri, 05 Jul 2019 18:57:34: Done! INFO @ Fri, 05 Jul 2019 18:57:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.05_summits.bed INFO @ Fri, 05 Jul 2019 18:57:34: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1313 records, 4 fields): 5 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1783 records, 4 fields): 6 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 18:57:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:57:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:57:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:57:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593995/ERX593995.20_summits.bed INFO @ Fri, 05 Jul 2019 18:57:53: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (833 records, 4 fields): 5 millis CompletedMACS2peakCalling