Job ID = 2006275 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,982,102 reads read : 2,982,102 reads written : 2,982,102 spots read : 2,922,659 reads read : 2,922,659 reads written : 2,922,659 spots read : 2,856,222 reads read : 2,856,222 reads written : 2,856,222 spots read : 2,849,741 reads read : 2,849,741 reads written : 2,849,741 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: 00:05:29 11610724 reads; of these: 11610724 (100.00%) were unpaired; of these: 602419 (5.19%) aligned 0 times 10000654 (86.13%) aligned exactly 1 time 1007651 (8.68%) aligned >1 times 94.81% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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_sort_core] merging from 8 files... [bam_rmdupse_core] 10352078 / 11008305 = 0.9404 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 15:31:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.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 15:31:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:31:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:31:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.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 15:31:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:31:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:32:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.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 15:32:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:32:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:32:07: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:32:07: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:32:07: #1 total tags in treatment: 656227 INFO @ Fri, 05 Jul 2019 15:32:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:32:07: #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 15:32:07: #1 tags after filtering in treatment: 656227 INFO @ Fri, 05 Jul 2019 15:32:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:32:07: #1 finished! INFO @ Fri, 05 Jul 2019 15:32:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:32:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:32:07: #2 number of paired peaks: 689 WARNING @ Fri, 05 Jul 2019 15:32:07: Fewer paired peaks (689) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 689 pairs to build model! INFO @ Fri, 05 Jul 2019 15:32:07: start model_add_line... INFO @ Fri, 05 Jul 2019 15:32:07: start X-correlation... INFO @ Fri, 05 Jul 2019 15:32:07: end of X-cor INFO @ Fri, 05 Jul 2019 15:32:07: #2 finished! INFO @ Fri, 05 Jul 2019 15:32:07: #2 predicted fragment length is 192 bps INFO @ Fri, 05 Jul 2019 15:32:07: #2 alternative fragment length(s) may be 192 bps INFO @ Fri, 05 Jul 2019 15:32:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.05_model.r INFO @ Fri, 05 Jul 2019 15:32:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:32:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:32:07: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:32:07: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:32:07: #1 total tags in treatment: 656227 INFO @ Fri, 05 Jul 2019 15:32:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:32:07: #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 15:32:07: #1 tags after filtering in treatment: 656227 INFO @ Fri, 05 Jul 2019 15:32:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:32:07: #1 finished! INFO @ Fri, 05 Jul 2019 15:32:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:32:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:32:08: #2 number of paired peaks: 689 WARNING @ Fri, 05 Jul 2019 15:32:08: Fewer paired peaks (689) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 689 pairs to build model! INFO @ Fri, 05 Jul 2019 15:32:08: start model_add_line... INFO @ Fri, 05 Jul 2019 15:32:08: start X-correlation... INFO @ Fri, 05 Jul 2019 15:32:08: end of X-cor INFO @ Fri, 05 Jul 2019 15:32:08: #2 finished! INFO @ Fri, 05 Jul 2019 15:32:08: #2 predicted fragment length is 192 bps INFO @ Fri, 05 Jul 2019 15:32:08: #2 alternative fragment length(s) may be 192 bps INFO @ Fri, 05 Jul 2019 15:32:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.20_model.r INFO @ Fri, 05 Jul 2019 15:32:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:32:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:32:08: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:32:08: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:32:08: #1 total tags in treatment: 656227 INFO @ Fri, 05 Jul 2019 15:32:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:32:08: #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 15:32:08: #1 tags after filtering in treatment: 656227 INFO @ Fri, 05 Jul 2019 15:32:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:32:08: #1 finished! INFO @ Fri, 05 Jul 2019 15:32:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:32:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:32:08: #2 number of paired peaks: 689 WARNING @ Fri, 05 Jul 2019 15:32:08: Fewer paired peaks (689) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 689 pairs to build model! INFO @ Fri, 05 Jul 2019 15:32:08: start model_add_line... INFO @ Fri, 05 Jul 2019 15:32:08: start X-correlation... INFO @ Fri, 05 Jul 2019 15:32:08: end of X-cor INFO @ Fri, 05 Jul 2019 15:32:08: #2 finished! INFO @ Fri, 05 Jul 2019 15:32:08: #2 predicted fragment length is 192 bps INFO @ Fri, 05 Jul 2019 15:32:08: #2 alternative fragment length(s) may be 192 bps INFO @ Fri, 05 Jul 2019 15:32:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.10_model.r INFO @ Fri, 05 Jul 2019 15:32:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:32:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:32:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:32:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:32:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:32:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:32:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.05_summits.bed INFO @ Fri, 05 Jul 2019 15:32:11: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (961 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 15:32:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:32:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:32:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:32:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.20_summits.bed INFO @ Fri, 05 Jul 2019 15:32:12: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (557 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:32:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:32:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:32:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548127/ERX2548127.10_summits.bed INFO @ Fri, 05 Jul 2019 15:32:12: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (754 records, 4 fields): 6 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。