Job ID = 2009026 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,652,625 reads read : 8,652,625 reads written : 8,652,625 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637560.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: 00:01:25 8652625 reads; of these: 8652625 (100.00%) were unpaired; of these: 336400 (3.89%) aligned 0 times 6888136 (79.61%) aligned exactly 1 time 1428089 (16.50%) aligned >1 times 96.11% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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] 4763450 / 8316225 = 0.5728 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 19:13:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.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 19:13:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:13:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:13:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.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 19:13:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:13:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:13:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.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 19:13:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:13:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:13:37: 1000000 INFO @ Fri, 05 Jul 2019 19:13:37: 1000000 INFO @ Fri, 05 Jul 2019 19:13:39: 1000000 INFO @ Fri, 05 Jul 2019 19:13:45: 2000000 INFO @ Fri, 05 Jul 2019 19:13:45: 2000000 INFO @ Fri, 05 Jul 2019 19:13:47: 2000000 INFO @ Fri, 05 Jul 2019 19:13:53: 3000000 INFO @ Fri, 05 Jul 2019 19:13:53: 3000000 INFO @ Fri, 05 Jul 2019 19:13:54: 3000000 INFO @ Fri, 05 Jul 2019 19:13:57: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:13:57: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:13:57: #1 total tags in treatment: 3552775 INFO @ Fri, 05 Jul 2019 19:13:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:13:57: #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 19:13:57: #1 tags after filtering in treatment: 3552775 INFO @ Fri, 05 Jul 2019 19:13:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:13:57: #1 finished! INFO @ Fri, 05 Jul 2019 19:13:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:13:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:13:57: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:13:57: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:13:57: #1 total tags in treatment: 3552775 INFO @ Fri, 05 Jul 2019 19:13:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:13:57: #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 19:13:58: #1 tags after filtering in treatment: 3552775 INFO @ Fri, 05 Jul 2019 19:13:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:13:58: #1 finished! INFO @ Fri, 05 Jul 2019 19:13:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:13:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:13:58: #2 number of paired peaks: 177 WARNING @ Fri, 05 Jul 2019 19:13:58: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 05 Jul 2019 19:13:58: start model_add_line... INFO @ Fri, 05 Jul 2019 19:13:58: start X-correlation... INFO @ Fri, 05 Jul 2019 19:13:58: end of X-cor INFO @ Fri, 05 Jul 2019 19:13:58: #2 finished! INFO @ Fri, 05 Jul 2019 19:13:58: #2 predicted fragment length is 93 bps INFO @ Fri, 05 Jul 2019 19:13:58: #2 alternative fragment length(s) may be 4,83,93 bps INFO @ Fri, 05 Jul 2019 19:13:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.05_model.r INFO @ Fri, 05 Jul 2019 19:13:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:13:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:13:58: #2 number of paired peaks: 177 WARNING @ Fri, 05 Jul 2019 19:13:58: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 05 Jul 2019 19:13:58: start model_add_line... INFO @ Fri, 05 Jul 2019 19:13:58: start X-correlation... INFO @ Fri, 05 Jul 2019 19:13:58: end of X-cor INFO @ Fri, 05 Jul 2019 19:13:58: #2 finished! INFO @ Fri, 05 Jul 2019 19:13:58: #2 predicted fragment length is 93 bps INFO @ Fri, 05 Jul 2019 19:13:58: #2 alternative fragment length(s) may be 4,83,93 bps INFO @ Fri, 05 Jul 2019 19:13:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.10_model.r INFO @ Fri, 05 Jul 2019 19:13:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:13:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:13:58: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 19:13:58: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 19:13:58: #1 total tags in treatment: 3552775 INFO @ Fri, 05 Jul 2019 19:13:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:13:58: #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 19:13:58: #1 tags after filtering in treatment: 3552775 INFO @ Fri, 05 Jul 2019 19:13:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:13:58: #1 finished! INFO @ Fri, 05 Jul 2019 19:13:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:13:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:13:59: #2 number of paired peaks: 177 WARNING @ Fri, 05 Jul 2019 19:13:59: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 05 Jul 2019 19:13:59: start model_add_line... INFO @ Fri, 05 Jul 2019 19:13:59: start X-correlation... INFO @ Fri, 05 Jul 2019 19:13:59: end of X-cor INFO @ Fri, 05 Jul 2019 19:13:59: #2 finished! INFO @ Fri, 05 Jul 2019 19:13:59: #2 predicted fragment length is 93 bps INFO @ Fri, 05 Jul 2019 19:13:59: #2 alternative fragment length(s) may be 4,83,93 bps INFO @ Fri, 05 Jul 2019 19:13:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.20_model.r INFO @ Fri, 05 Jul 2019 19:13:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:14:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:14:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:14:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:14:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:14:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:14:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:14:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:14:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.05_summits.bed INFO @ Fri, 05 Jul 2019 19:14:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.10_summits.bed INFO @ Fri, 05 Jul 2019 19:14:12: Done! INFO @ Fri, 05 Jul 2019 19:14:12: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (6155 records, 4 fields): 13 millis INFO @ Fri, 05 Jul 2019 19:14:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:14:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:14:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594041/ERX594041.20_summits.bed INFO @ Fri, 05 Jul 2019 19:14:13: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (2572 records, 4 fields): 7 millis CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (4470 records, 4 fields): 11 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。