Job ID = 2006002 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 470,465 reads read : 470,465 reads written : 470,465 spots read : 445,720 reads read : 445,720 reads written : 445,720 spots read : 457,560 reads read : 457,560 reads written : 457,560 spots read : 449,409 reads read : 449,409 reads written : 449,409 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529266.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529267.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529268.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:05 1823154 reads; of these: 1823154 (100.00%) were unpaired; of these: 82027 (4.50%) aligned 0 times 1429972 (78.43%) aligned exactly 1 time 311155 (17.07%) aligned >1 times 95.50% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 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] 1549777 / 1741127 = 0.8901 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 14:47:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.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 14:47:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:47:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:47:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.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 14:47:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:47:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:47:16: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 14:47:16: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 14:47:16: #1 total tags in treatment: 191350 INFO @ Fri, 05 Jul 2019 14:47:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:47:16: #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 14:47:16: #1 tags after filtering in treatment: 191350 INFO @ Fri, 05 Jul 2019 14:47:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:47:16: #1 finished! INFO @ Fri, 05 Jul 2019 14:47:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:47:16: #2 number of paired peaks: 156 WARNING @ Fri, 05 Jul 2019 14:47:16: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 05 Jul 2019 14:47:16: start model_add_line... INFO @ Fri, 05 Jul 2019 14:47:16: start X-correlation... INFO @ Fri, 05 Jul 2019 14:47:16: end of X-cor INFO @ Fri, 05 Jul 2019 14:47:16: #2 finished! INFO @ Fri, 05 Jul 2019 14:47:16: #2 predicted fragment length is 185 bps INFO @ Fri, 05 Jul 2019 14:47:16: #2 alternative fragment length(s) may be 63,82,123,130,136,144,148,185,205,262,332,587 bps INFO @ Fri, 05 Jul 2019 14:47:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.05_model.r INFO @ Fri, 05 Jul 2019 14:47:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:47:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:47:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.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 14:47:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:47:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:47:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:47:17: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 14:47:17: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 14:47:17: #1 total tags in treatment: 191350 INFO @ Fri, 05 Jul 2019 14:47:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:47:17: #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 14:47:17: #1 tags after filtering in treatment: 191350 INFO @ Fri, 05 Jul 2019 14:47:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:47:17: #1 finished! INFO @ Fri, 05 Jul 2019 14:47:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:47:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:47:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:47:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:47:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.05_summits.bed INFO @ Fri, 05 Jul 2019 14:47:17: Done! INFO @ Fri, 05 Jul 2019 14:47:17: #2 number of paired peaks: 156 WARNING @ Fri, 05 Jul 2019 14:47:17: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 05 Jul 2019 14:47:17: start model_add_line... INFO @ Fri, 05 Jul 2019 14:47:17: start X-correlation... INFO @ Fri, 05 Jul 2019 14:47:17: end of X-cor INFO @ Fri, 05 Jul 2019 14:47:17: #2 finished! INFO @ Fri, 05 Jul 2019 14:47:17: #2 predicted fragment length is 185 bps INFO @ Fri, 05 Jul 2019 14:47:17: #2 alternative fragment length(s) may be 63,82,123,130,136,144,148,185,205,262,332,587 bps INFO @ Fri, 05 Jul 2019 14:47:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.10_model.r INFO @ Fri, 05 Jul 2019 14:47:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:47:17: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 14:47:18: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 14:47:18: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 14:47:18: #1 total tags in treatment: 191350 INFO @ Fri, 05 Jul 2019 14:47:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:47:18: #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 14:47:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:47:18: #1 tags after filtering in treatment: 191350 INFO @ Fri, 05 Jul 2019 14:47:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:47:18: #1 finished! INFO @ Fri, 05 Jul 2019 14:47:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:47:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:47:18: #2 number of paired peaks: 156 WARNING @ Fri, 05 Jul 2019 14:47:18: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 05 Jul 2019 14:47:18: start model_add_line... INFO @ Fri, 05 Jul 2019 14:47:18: start X-correlation... INFO @ Fri, 05 Jul 2019 14:47:18: end of X-cor INFO @ Fri, 05 Jul 2019 14:47:18: #2 finished! INFO @ Fri, 05 Jul 2019 14:47:18: #2 predicted fragment length is 185 bps INFO @ Fri, 05 Jul 2019 14:47:18: #2 alternative fragment length(s) may be 63,82,123,130,136,144,148,185,205,262,332,587 bps INFO @ Fri, 05 Jul 2019 14:47:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.20_model.r INFO @ Fri, 05 Jul 2019 14:47:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:47:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 14:47:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:47:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:47:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.10_summits.bed INFO @ Fri, 05 Jul 2019 14:47:18: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 14:47:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:47:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.20_peaks.xls BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 14:47:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:47:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548088/ERX2548088.20_summits.bed INFO @ Fri, 05 Jul 2019 14:47:19: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (5 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling