Job ID = 2008229 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,878,725 reads read : 17,757,450 reads written : 17,757,450 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628952.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: 00:16:25 8878725 reads; of these: 8878725 (100.00%) were paired; of these: 685933 (7.73%) aligned concordantly 0 times 7545207 (84.98%) aligned concordantly exactly 1 time 647585 (7.29%) aligned concordantly >1 times ---- 685933 pairs aligned concordantly 0 times; of these: 54982 (8.02%) aligned discordantly 1 time ---- 630951 pairs aligned 0 times concordantly or discordantly; of these: 1261902 mates make up the pairs; of these: 1208032 (95.73%) aligned 0 times 31631 (2.51%) aligned exactly 1 time 22239 (1.76%) aligned >1 times 93.20% overall alignment rate Time searching: 00:16:25 Overall time: 00:16:25 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_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 7849413 / 8236699 = 0.9530 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 18:09:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.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 18:09:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:09:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.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 18:09:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:09:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:09:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.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 18:09:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:09:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:10:03: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:10:03: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:10:03: #1 total tags in treatment: 392389 INFO @ Fri, 05 Jul 2019 18:10:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:10:03: #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 18:10:03: #1 tags after filtering in treatment: 332869 INFO @ Fri, 05 Jul 2019 18:10:03: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 05 Jul 2019 18:10:03: #1 finished! INFO @ Fri, 05 Jul 2019 18:10:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:10:03: #2 number of paired peaks: 335 WARNING @ Fri, 05 Jul 2019 18:10:03: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Fri, 05 Jul 2019 18:10:03: start model_add_line... INFO @ Fri, 05 Jul 2019 18:10:03: start X-correlation... INFO @ Fri, 05 Jul 2019 18:10:03: end of X-cor INFO @ Fri, 05 Jul 2019 18:10:03: #2 finished! INFO @ Fri, 05 Jul 2019 18:10:03: #2 predicted fragment length is 165 bps INFO @ Fri, 05 Jul 2019 18:10:03: #2 alternative fragment length(s) may be 15,96,165,196,235,466,575,588 bps INFO @ Fri, 05 Jul 2019 18:10:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.05_model.r INFO @ Fri, 05 Jul 2019 18:10:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:10:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:10:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:10:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:10:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:10:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.05_summits.bed INFO @ Fri, 05 Jul 2019 18:10:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 18:10:05: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:10:05: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:10:05: #1 total tags in treatment: 392389 INFO @ Fri, 05 Jul 2019 18:10:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:10:05: #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 18:10:05: #1 tags after filtering in treatment: 332869 INFO @ Fri, 05 Jul 2019 18:10:05: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 05 Jul 2019 18:10:05: #1 finished! INFO @ Fri, 05 Jul 2019 18:10:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:10:05: #2 number of paired peaks: 335 WARNING @ Fri, 05 Jul 2019 18:10:05: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Fri, 05 Jul 2019 18:10:05: start model_add_line... INFO @ Fri, 05 Jul 2019 18:10:05: start X-correlation... INFO @ Fri, 05 Jul 2019 18:10:05: end of X-cor INFO @ Fri, 05 Jul 2019 18:10:05: #2 finished! INFO @ Fri, 05 Jul 2019 18:10:05: #2 predicted fragment length is 165 bps INFO @ Fri, 05 Jul 2019 18:10:05: #2 alternative fragment length(s) may be 15,96,165,196,235,466,575,588 bps INFO @ Fri, 05 Jul 2019 18:10:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.20_model.r INFO @ Fri, 05 Jul 2019 18:10:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:10:06: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:10:06: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:10:06: #1 total tags in treatment: 392389 INFO @ Fri, 05 Jul 2019 18:10:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:10:06: #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 18:10:06: #1 tags after filtering in treatment: 332869 INFO @ Fri, 05 Jul 2019 18:10:06: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 05 Jul 2019 18:10:06: #1 finished! INFO @ Fri, 05 Jul 2019 18:10:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:10:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:10:06: #2 number of paired peaks: 335 WARNING @ Fri, 05 Jul 2019 18:10:06: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Fri, 05 Jul 2019 18:10:06: start model_add_line... INFO @ Fri, 05 Jul 2019 18:10:06: start X-correlation... INFO @ Fri, 05 Jul 2019 18:10:06: end of X-cor INFO @ Fri, 05 Jul 2019 18:10:06: #2 finished! INFO @ Fri, 05 Jul 2019 18:10:06: #2 predicted fragment length is 165 bps INFO @ Fri, 05 Jul 2019 18:10:06: #2 alternative fragment length(s) may be 15,96,165,196,235,466,575,588 bps INFO @ Fri, 05 Jul 2019 18:10:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.10_model.r INFO @ Fri, 05 Jul 2019 18:10:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:10:06: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:10:06: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:10:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:10:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:10:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:10:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.20_summits.bed INFO @ Fri, 05 Jul 2019 18:10:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 18:10:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:10:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:10:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585753/ERX585753.10_summits.bed INFO @ Fri, 05 Jul 2019 18:10:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (32 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。