Job ID = 2006632 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,994,061 reads read : 1,994,061 reads written : 1,994,061 spots read : 1,888,270 reads read : 1,888,270 reads written : 1,888,270 spots read : 1,940,299 reads read : 1,940,299 reads written : 1,940,299 spots read : 1,906,922 reads read : 1,906,922 reads written : 1,906,922 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529562.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529563.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529564.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529565.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: 00:03:13 7729552 reads; of these: 7729552 (100.00%) were unpaired; of these: 293545 (3.80%) aligned 0 times 6336602 (81.98%) aligned exactly 1 time 1099405 (14.22%) aligned >1 times 96.20% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 6778531 / 7436007 = 0.9116 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 15:46:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.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 15:46:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:46:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:46:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.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 15:46:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:46:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:46:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.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 15:46:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:46:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:46:53: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:46:53: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:46:53: #1 total tags in treatment: 657476 INFO @ Fri, 05 Jul 2019 15:46:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:46:53: #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 15:46:53: #1 tags after filtering in treatment: 657476 INFO @ Fri, 05 Jul 2019 15:46:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:46:53: #1 finished! INFO @ Fri, 05 Jul 2019 15:46:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:46:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:46:53: #2 number of paired peaks: 264 WARNING @ Fri, 05 Jul 2019 15:46:53: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Fri, 05 Jul 2019 15:46:53: start model_add_line... INFO @ Fri, 05 Jul 2019 15:46:53: start X-correlation... INFO @ Fri, 05 Jul 2019 15:46:53: end of X-cor INFO @ Fri, 05 Jul 2019 15:46:53: #2 finished! INFO @ Fri, 05 Jul 2019 15:46:53: #2 predicted fragment length is 197 bps INFO @ Fri, 05 Jul 2019 15:46:53: #2 alternative fragment length(s) may be 1,22,42,64,80,98,127,172,197,234,267,303,560 bps INFO @ Fri, 05 Jul 2019 15:46:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.05_model.r INFO @ Fri, 05 Jul 2019 15:46:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:46:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:46:55: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:46:55: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:46:55: #1 total tags in treatment: 657476 INFO @ Fri, 05 Jul 2019 15:46:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:46:55: #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 15:46:55: #1 tags after filtering in treatment: 657476 INFO @ Fri, 05 Jul 2019 15:46:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:46:55: #1 finished! INFO @ Fri, 05 Jul 2019 15:46:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:46:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:46:55: #2 number of paired peaks: 264 WARNING @ Fri, 05 Jul 2019 15:46:55: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Fri, 05 Jul 2019 15:46:55: start model_add_line... INFO @ Fri, 05 Jul 2019 15:46:55: start X-correlation... INFO @ Fri, 05 Jul 2019 15:46:55: end of X-cor INFO @ Fri, 05 Jul 2019 15:46:55: #2 finished! INFO @ Fri, 05 Jul 2019 15:46:55: #2 predicted fragment length is 197 bps INFO @ Fri, 05 Jul 2019 15:46:55: #2 alternative fragment length(s) may be 1,22,42,64,80,98,127,172,197,234,267,303,560 bps INFO @ Fri, 05 Jul 2019 15:46:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.10_model.r INFO @ Fri, 05 Jul 2019 15:46:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:46:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:46:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:46:56: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:46:56: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:46:56: #1 total tags in treatment: 657476 INFO @ Fri, 05 Jul 2019 15:46:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:46:56: #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 15:46:56: #1 tags after filtering in treatment: 657476 INFO @ Fri, 05 Jul 2019 15:46:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:46:56: #1 finished! INFO @ Fri, 05 Jul 2019 15:46:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:46:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:46:56: #2 number of paired peaks: 264 WARNING @ Fri, 05 Jul 2019 15:46:56: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Fri, 05 Jul 2019 15:46:56: start model_add_line... INFO @ Fri, 05 Jul 2019 15:46:56: start X-correlation... INFO @ Fri, 05 Jul 2019 15:46:56: end of X-cor INFO @ Fri, 05 Jul 2019 15:46:56: #2 finished! INFO @ Fri, 05 Jul 2019 15:46:56: #2 predicted fragment length is 197 bps INFO @ Fri, 05 Jul 2019 15:46:56: #2 alternative fragment length(s) may be 1,22,42,64,80,98,127,172,197,234,267,303,560 bps INFO @ Fri, 05 Jul 2019 15:46:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.20_model.r INFO @ Fri, 05 Jul 2019 15:46:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:46:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:46:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:46:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:46:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.05_summits.bed INFO @ Fri, 05 Jul 2019 15:46:57: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:46:57: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:46:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:46:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:46:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.10_summits.bed INFO @ Fri, 05 Jul 2019 15:46:58: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:46:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:47:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:47:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:47:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548174/ERX2548174.20_summits.bed INFO @ Fri, 05 Jul 2019 15:47:00: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。