Job ID = 2009036 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,006,978 reads read : 10,006,978 reads written : 10,006,978 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637603.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 10006978 reads; of these: 10006978 (100.00%) were unpaired; of these: 5846876 (58.43%) aligned 0 times 3431078 (34.29%) aligned exactly 1 time 729024 (7.29%) aligned >1 times 41.57% 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] 2083571 / 4160102 = 0.5008 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 19:15:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.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 19:15:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:15:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:15:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.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 19:15:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:15:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:15:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.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 19:15:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:15:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:15:31: 1000000 INFO @ Fri, 05 Jul 2019 19:15:31: 1000000 INFO @ Fri, 05 Jul 2019 19:15:33: 1000000 INFO @ Fri, 05 Jul 2019 19:15:39: 2000000 INFO @ Fri, 05 Jul 2019 19:15:39: 2000000 INFO @ Fri, 05 Jul 2019 19:15:40: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:15:40: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:15:40: #1 total tags in treatment: 2076531 INFO @ Fri, 05 Jul 2019 19:15:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:15:40: #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 19:15:40: #1 tags after filtering in treatment: 2076531 INFO @ Fri, 05 Jul 2019 19:15:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:15:40: #1 finished! INFO @ Fri, 05 Jul 2019 19:15:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:15:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:15:40: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:15:40: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:15:40: #1 total tags in treatment: 2076531 INFO @ Fri, 05 Jul 2019 19:15:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:15:40: #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 19:15:40: #1 tags after filtering in treatment: 2076531 INFO @ Fri, 05 Jul 2019 19:15:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:15:40: #1 finished! INFO @ Fri, 05 Jul 2019 19:15:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:15:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:15:40: #2 number of paired peaks: 381 WARNING @ Fri, 05 Jul 2019 19:15:40: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 05 Jul 2019 19:15:40: start model_add_line... INFO @ Fri, 05 Jul 2019 19:15:40: start X-correlation... INFO @ Fri, 05 Jul 2019 19:15:40: end of X-cor INFO @ Fri, 05 Jul 2019 19:15:40: #2 finished! INFO @ Fri, 05 Jul 2019 19:15:40: #2 predicted fragment length is 158 bps INFO @ Fri, 05 Jul 2019 19:15:40: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 05 Jul 2019 19:15:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.05_model.r INFO @ Fri, 05 Jul 2019 19:15:40: #2 number of paired peaks: 381 WARNING @ Fri, 05 Jul 2019 19:15:40: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 05 Jul 2019 19:15:40: start model_add_line... INFO @ Fri, 05 Jul 2019 19:15:40: start X-correlation... INFO @ Fri, 05 Jul 2019 19:15:40: end of X-cor INFO @ Fri, 05 Jul 2019 19:15:40: #2 finished! INFO @ Fri, 05 Jul 2019 19:15:40: #2 predicted fragment length is 158 bps INFO @ Fri, 05 Jul 2019 19:15:40: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 05 Jul 2019 19:15:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.10_model.r INFO @ Fri, 05 Jul 2019 19:15:42: 2000000 INFO @ Fri, 05 Jul 2019 19:15:42: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:15:42: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:15:42: #1 total tags in treatment: 2076531 INFO @ Fri, 05 Jul 2019 19:15:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:15:42: #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 19:15:42: #1 tags after filtering in treatment: 2076531 INFO @ Fri, 05 Jul 2019 19:15:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:15:42: #1 finished! INFO @ Fri, 05 Jul 2019 19:15:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:15:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:15:43: #2 number of paired peaks: 381 WARNING @ Fri, 05 Jul 2019 19:15:43: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 05 Jul 2019 19:15:43: start model_add_line... INFO @ Fri, 05 Jul 2019 19:15:43: start X-correlation... INFO @ Fri, 05 Jul 2019 19:15:43: end of X-cor INFO @ Fri, 05 Jul 2019 19:15:43: #2 finished! INFO @ Fri, 05 Jul 2019 19:15:43: #2 predicted fragment length is 158 bps INFO @ Fri, 05 Jul 2019 19:15:43: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 05 Jul 2019 19:15:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.20_model.r INFO @ Fri, 05 Jul 2019 19:15:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:15:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:15:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:15:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:15:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:15:56: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:15:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:16:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:16:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:16:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.20_peaks.narrowPeak BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 19:16:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.20_summits.bed INFO @ Fri, 05 Jul 2019 19:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.10_summits.bed INFO @ Fri, 05 Jul 2019 19:16:03: Done! INFO @ Fri, 05 Jul 2019 19:16:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:16:04: Done! pass1 - making usageList (16 chroms): 2 millis pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1833 records, 4 fields): 304 millis pass2 - checking and writing primary data (2516 records, 4 fields): 405 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:16:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594048/ERX594048.05_summits.bed INFO @ Fri, 05 Jul 2019 19:16:08: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (3180 records, 4 fields): 10 millis CompletedMACS2peakCalling CompletedMACS2peakCalling