Job ID = 2007640 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,201,528 reads read : 2,201,528 reads written : 2,201,528 spots read : 2,115,220 reads read : 2,115,220 reads written : 2,115,220 spots read : 2,164,031 reads read : 2,164,031 reads written : 2,164,031 spots read : 2,081,259 reads read : 2,081,259 reads written : 2,081,259 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529774.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529775.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529776.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529777.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: 00:04:15 8562038 reads; of these: 8562038 (100.00%) were unpaired; of these: 1481178 (17.30%) aligned 0 times 5907482 (69.00%) aligned exactly 1 time 1173378 (13.70%) aligned >1 times 82.70% overall alignment rate Time searching: 00:04:17 Overall time: 00:04:17 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] 6725797 / 7080860 = 0.9499 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 16:13:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.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 16:13:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.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 16:13:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.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 16:13:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:42: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:13:42: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:13:42: #1 total tags in treatment: 355063 INFO @ Fri, 05 Jul 2019 16:13:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:42: #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 16:13:42: #1 tags after filtering in treatment: 355063 INFO @ Fri, 05 Jul 2019 16:13:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:42: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:13:42: #2 number of paired peaks: 461 WARNING @ Fri, 05 Jul 2019 16:13:42: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:42: start model_add_line... INFO @ Fri, 05 Jul 2019 16:13:42: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:42: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:42: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:42: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 16:13:42: #2 alternative fragment length(s) may be 110,132,156,180,556,585 bps INFO @ Fri, 05 Jul 2019 16:13:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.05_model.r WARNING @ Fri, 05 Jul 2019 16:13:42: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:13:42: #2 You may need to consider one of the other alternative d(s): 110,132,156,180,556,585 WARNING @ Fri, 05 Jul 2019 16:13:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:13:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:13:43: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:13:43: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:13:43: #1 total tags in treatment: 355063 INFO @ Fri, 05 Jul 2019 16:13:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:43: #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 16:13:43: #1 tags after filtering in treatment: 355063 INFO @ Fri, 05 Jul 2019 16:13:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:43: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:13:43: #2 number of paired peaks: 461 WARNING @ Fri, 05 Jul 2019 16:13:43: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:43: start model_add_line... INFO @ Fri, 05 Jul 2019 16:13:43: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:43: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:43: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:43: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 16:13:43: #2 alternative fragment length(s) may be 110,132,156,180,556,585 bps INFO @ Fri, 05 Jul 2019 16:13:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.10_model.r WARNING @ Fri, 05 Jul 2019 16:13:43: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:13:43: #2 You may need to consider one of the other alternative d(s): 110,132,156,180,556,585 WARNING @ Fri, 05 Jul 2019 16:13:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:13:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:13:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:13:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.05_summits.bed INFO @ Fri, 05 Jul 2019 16:13:44: Done! INFO @ Fri, 05 Jul 2019 16:13:44: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:13:44: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:13:44: #1 total tags in treatment: 355063 INFO @ Fri, 05 Jul 2019 16:13:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:44: #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 16:13:44: #1 tags after filtering in treatment: 355063 INFO @ Fri, 05 Jul 2019 16:13:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:44: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:44: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (17 chroms): 1 millis INFO @ Fri, 05 Jul 2019 16:13:44: #2 number of paired peaks: 461 WARNING @ Fri, 05 Jul 2019 16:13:44: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:44: start model_add_line... pass2 - checking and writing primary data (196 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:13:44: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:44: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:44: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:44: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 16:13:44: #2 alternative fragment length(s) may be 110,132,156,180,556,585 bps INFO @ Fri, 05 Jul 2019 16:13:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.20_model.r WARNING @ Fri, 05 Jul 2019 16:13:44: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:13:44: #2 You may need to consider one of the other alternative d(s): 110,132,156,180,556,585 WARNING @ Fri, 05 Jul 2019 16:13:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:13:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:13:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:13:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.10_summits.bed INFO @ Fri, 05 Jul 2019 16:13:45: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (76 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:13:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:13:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548239/ERX2548239.20_summits.bed INFO @ Fri, 05 Jul 2019 16:13:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (27 records, 4 fields): 2 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。