Job ID = 2008992 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,798,063 reads read : 6,798,063 reads written : 6,798,063 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637567.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: 00:00:53 6798063 reads; of these: 6798063 (100.00%) were unpaired; of these: 2968018 (43.66%) aligned 0 times 2741074 (40.32%) aligned exactly 1 time 1088971 (16.02%) aligned >1 times 56.34% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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] 1937837 / 3830045 = 0.5060 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 19:02:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.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 19:02:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:02:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:02:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.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 19:02:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:02:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:03:08: 1000000 INFO @ Fri, 05 Jul 2019 19:03:08: 1000000 INFO @ Fri, 05 Jul 2019 19:03:17: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:03:17: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:03:17: #1 total tags in treatment: 1892208 INFO @ Fri, 05 Jul 2019 19:03:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:03:17: #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 19:03:17: #1 tags after filtering in treatment: 1892208 INFO @ Fri, 05 Jul 2019 19:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:03:17: #1 finished! INFO @ Fri, 05 Jul 2019 19:03:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:03:17: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:03:17: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:03:17: #1 total tags in treatment: 1892208 INFO @ Fri, 05 Jul 2019 19:03:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:03:17: #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 19:03:17: #1 tags after filtering in treatment: 1892208 INFO @ Fri, 05 Jul 2019 19:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:03:17: #1 finished! INFO @ Fri, 05 Jul 2019 19:03:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:03:17: #2 number of paired peaks: 392 WARNING @ Fri, 05 Jul 2019 19:03:17: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Fri, 05 Jul 2019 19:03:17: start model_add_line... INFO @ Fri, 05 Jul 2019 19:03:17: start X-correlation... INFO @ Fri, 05 Jul 2019 19:03:17: end of X-cor INFO @ Fri, 05 Jul 2019 19:03:17: #2 finished! INFO @ Fri, 05 Jul 2019 19:03:17: #2 predicted fragment length is 163 bps INFO @ Fri, 05 Jul 2019 19:03:17: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 05 Jul 2019 19:03:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.05_model.r INFO @ Fri, 05 Jul 2019 19:03:17: #2 number of paired peaks: 392 WARNING @ Fri, 05 Jul 2019 19:03:17: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Fri, 05 Jul 2019 19:03:17: start model_add_line... INFO @ Fri, 05 Jul 2019 19:03:17: start X-correlation... INFO @ Fri, 05 Jul 2019 19:03:17: end of X-cor INFO @ Fri, 05 Jul 2019 19:03:17: #2 finished! INFO @ Fri, 05 Jul 2019 19:03:17: #2 predicted fragment length is 163 bps INFO @ Fri, 05 Jul 2019 19:03:17: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 05 Jul 2019 19:03:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.10_model.r INFO @ Fri, 05 Jul 2019 19:03:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:03:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:03:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:03:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:03:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.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 19:03:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:03:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:03:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:03:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:03:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.10_summits.bed INFO @ Fri, 05 Jul 2019 19:03:28: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (2417 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 19:03:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:03:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:03:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.05_summits.bed INFO @ Fri, 05 Jul 2019 19:03:28: Done! INFO @ Fri, 05 Jul 2019 19:03:30: 1000000 INFO @ Fri, 05 Jul 2019 19:03:38: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:03:38: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:03:38: #1 total tags in treatment: 1892208 INFO @ Fri, 05 Jul 2019 19:03:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:03:38: #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 19:03:38: #1 tags after filtering in treatment: 1892208 INFO @ Fri, 05 Jul 2019 19:03:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:03:38: #1 finished! INFO @ Fri, 05 Jul 2019 19:03:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:03:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:03:38: #2 number of paired peaks: 392 WARNING @ Fri, 05 Jul 2019 19:03:38: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Fri, 05 Jul 2019 19:03:38: start model_add_line... INFO @ Fri, 05 Jul 2019 19:03:38: start X-correlation... INFO @ Fri, 05 Jul 2019 19:03:38: end of X-cor INFO @ Fri, 05 Jul 2019 19:03:38: #2 finished! INFO @ Fri, 05 Jul 2019 19:03:38: #2 predicted fragment length is 163 bps INFO @ Fri, 05 Jul 2019 19:03:38: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 05 Jul 2019 19:03:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.20_model.r 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... pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (3050 records, 4 fields): 25 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:03:46: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:03:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:03:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.20_peaks.narrowPeak BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 19:04:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594013/ERX594013.20_summits.bed INFO @ Fri, 05 Jul 2019 19:04:10: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1715 records, 4 fields): 5 millis CompletedMACS2peakCalling