Job ID = 2007235 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,383,021 reads read : 2,383,021 reads written : 2,383,021 spots read : 2,278,511 reads read : 2,278,511 reads written : 2,278,511 spots read : 2,517,745 reads read : 2,517,745 reads written : 2,517,745 spots read : 2,269,736 reads read : 2,269,736 reads written : 2,269,736 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529662.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529663.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529664.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529665.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: 00:02:24 9449013 reads; of these: 9449013 (100.00%) were unpaired; of these: 376505 (3.98%) aligned 0 times 7627842 (80.73%) aligned exactly 1 time 1444666 (15.29%) aligned >1 times 96.02% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 8858165 / 9072508 = 0.9764 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 16:07:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.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 16:07:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:07:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:07:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.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 16:07:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:07:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:07:40: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:07:40: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:07:40: #1 total tags in treatment: 214343 INFO @ Fri, 05 Jul 2019 16:07:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:07:40: #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 16:07:40: #1 tags after filtering in treatment: 214343 INFO @ Fri, 05 Jul 2019 16:07:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:07:40: #1 finished! INFO @ Fri, 05 Jul 2019 16:07:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:07:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:07:40: #2 number of paired peaks: 387 WARNING @ Fri, 05 Jul 2019 16:07:40: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Fri, 05 Jul 2019 16:07:40: start model_add_line... INFO @ Fri, 05 Jul 2019 16:07:40: start X-correlation... INFO @ Fri, 05 Jul 2019 16:07:40: end of X-cor INFO @ Fri, 05 Jul 2019 16:07:40: #2 finished! INFO @ Fri, 05 Jul 2019 16:07:40: #2 predicted fragment length is 92 bps INFO @ Fri, 05 Jul 2019 16:07:40: #2 alternative fragment length(s) may be 22,47,92,117,148,178,238,291,311,343,363,423,450,565,580 bps INFO @ Fri, 05 Jul 2019 16:07:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.05_model.r WARNING @ Fri, 05 Jul 2019 16:07:40: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:07:40: #2 You may need to consider one of the other alternative d(s): 22,47,92,117,148,178,238,291,311,343,363,423,450,565,580 WARNING @ Fri, 05 Jul 2019 16:07:40: #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 16:07:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:07:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.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 16:07:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:07:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:07:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:07:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:07:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:07:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.05_summits.bed INFO @ Fri, 05 Jul 2019 16:07:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (56 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:07:41: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:07:41: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:07:41: #1 total tags in treatment: 214343 INFO @ Fri, 05 Jul 2019 16:07:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:07:41: #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 16:07:41: #1 tags after filtering in treatment: 214343 INFO @ Fri, 05 Jul 2019 16:07:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:07:41: #1 finished! INFO @ Fri, 05 Jul 2019 16:07:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:07:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:07:41: #2 number of paired peaks: 387 WARNING @ Fri, 05 Jul 2019 16:07:41: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Fri, 05 Jul 2019 16:07:41: start model_add_line... INFO @ Fri, 05 Jul 2019 16:07:41: start X-correlation... INFO @ Fri, 05 Jul 2019 16:07:41: end of X-cor INFO @ Fri, 05 Jul 2019 16:07:41: #2 finished! INFO @ Fri, 05 Jul 2019 16:07:41: #2 predicted fragment length is 92 bps INFO @ Fri, 05 Jul 2019 16:07:41: #2 alternative fragment length(s) may be 22,47,92,117,148,178,238,291,311,343,363,423,450,565,580 bps INFO @ Fri, 05 Jul 2019 16:07:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.10_model.r WARNING @ Fri, 05 Jul 2019 16:07:41: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:07:41: #2 You may need to consider one of the other alternative d(s): 22,47,92,117,148,178,238,291,311,343,363,423,450,565,580 WARNING @ Fri, 05 Jul 2019 16:07:41: #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 16:07:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:07:41: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:07:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:07:42: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:07:42: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:07:42: #1 total tags in treatment: 214343 INFO @ Fri, 05 Jul 2019 16:07:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:07:42: #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 16:07:42: #1 tags after filtering in treatment: 214343 INFO @ Fri, 05 Jul 2019 16:07:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:07:42: #1 finished! INFO @ Fri, 05 Jul 2019 16:07:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:07:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:07:42: #2 number of paired peaks: 387 WARNING @ Fri, 05 Jul 2019 16:07:42: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Fri, 05 Jul 2019 16:07:42: start model_add_line... INFO @ Fri, 05 Jul 2019 16:07:42: start X-correlation... INFO @ Fri, 05 Jul 2019 16:07:42: end of X-cor INFO @ Fri, 05 Jul 2019 16:07:42: #2 finished! INFO @ Fri, 05 Jul 2019 16:07:42: #2 predicted fragment length is 92 bps INFO @ Fri, 05 Jul 2019 16:07:42: #2 alternative fragment length(s) may be 22,47,92,117,148,178,238,291,311,343,363,423,450,565,580 bps INFO @ Fri, 05 Jul 2019 16:07:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.20_model.r INFO @ Fri, 05 Jul 2019 16:07:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:07:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:07:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.10_summits.bed INFO @ Fri, 05 Jul 2019 16:07:42: Done! WARNING @ Fri, 05 Jul 2019 16:07:42: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:07:42: #2 You may need to consider one of the other alternative d(s): 22,47,92,117,148,178,238,291,311,343,363,423,450,565,580 WARNING @ Fri, 05 Jul 2019 16:07:42: #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 16:07:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:07:42: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (17 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:07:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:07:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:07:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:07:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548205/ERX2548205.20_summits.bed INFO @ Fri, 05 Jul 2019 16:07:44: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 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。