Job ID = 2008270 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 99,568 reads read : 199,136 reads written : 199,136 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629051.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: 00:00:05 99568 reads; of these: 99568 (100.00%) were paired; of these: 3719 (3.74%) aligned concordantly 0 times 85353 (85.72%) aligned concordantly exactly 1 time 10496 (10.54%) aligned concordantly >1 times ---- 3719 pairs aligned concordantly 0 times; of these: 1772 (47.65%) aligned discordantly 1 time ---- 1947 pairs aligned 0 times concordantly or discordantly; of these: 3894 mates make up the pairs; of these: 2093 (53.75%) aligned 0 times 559 (14.36%) aligned exactly 1 time 1242 (31.90%) aligned >1 times 98.95% overall alignment rate Time searching: 00:00:05 Overall time: 00:00:05 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_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] 91079 / 97109 = 0.9379 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 18:13:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.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 18:13:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:13:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:13:05: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:13:05: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:13:05: #1 total tags in treatment: 6197 INFO @ Fri, 05 Jul 2019 18:13:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:13:05: #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 18:13:05: #1 tags after filtering in treatment: 5755 INFO @ Fri, 05 Jul 2019 18:13:05: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 18:13:05: #1 finished! INFO @ Fri, 05 Jul 2019 18:13:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:13:05: #2 number of paired peaks: 228 WARNING @ Fri, 05 Jul 2019 18:13:05: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Fri, 05 Jul 2019 18:13:05: start model_add_line... INFO @ Fri, 05 Jul 2019 18:13:05: start X-correlation... INFO @ Fri, 05 Jul 2019 18:13:05: end of X-cor INFO @ Fri, 05 Jul 2019 18:13:05: #2 finished! INFO @ Fri, 05 Jul 2019 18:13:05: #2 predicted fragment length is 292 bps INFO @ Fri, 05 Jul 2019 18:13:05: #2 alternative fragment length(s) may be 11,55,117,153,185,229,268,292,392,442,488,568,590 bps INFO @ Fri, 05 Jul 2019 18:13:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.05_model.r INFO @ Fri, 05 Jul 2019 18:13:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:13:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:13:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:13:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:13:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.05_summits.bed INFO @ Fri, 05 Jul 2019 18:13:05: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 18:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.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 18:13:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:13:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:13:06: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:13:06: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:13:06: #1 total tags in treatment: 6197 INFO @ Fri, 05 Jul 2019 18:13:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:13:06: #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 18:13:06: #1 tags after filtering in treatment: 5755 INFO @ Fri, 05 Jul 2019 18:13:06: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 18:13:06: #1 finished! INFO @ Fri, 05 Jul 2019 18:13:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:13:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:13:06: #2 number of paired peaks: 228 WARNING @ Fri, 05 Jul 2019 18:13:06: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Fri, 05 Jul 2019 18:13:06: start model_add_line... INFO @ Fri, 05 Jul 2019 18:13:06: start X-correlation... INFO @ Fri, 05 Jul 2019 18:13:06: end of X-cor INFO @ Fri, 05 Jul 2019 18:13:06: #2 finished! INFO @ Fri, 05 Jul 2019 18:13:06: #2 predicted fragment length is 292 bps INFO @ Fri, 05 Jul 2019 18:13:06: #2 alternative fragment length(s) may be 11,55,117,153,185,229,268,292,392,442,488,568,590 bps INFO @ Fri, 05 Jul 2019 18:13:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.10_model.r INFO @ Fri, 05 Jul 2019 18:13:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:13:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:13:06: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:13:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:13:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:13:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.10_summits.bed INFO @ Fri, 05 Jul 2019 18:13:06: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:13:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.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 18:13:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:13:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:13:07: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:13:07: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:13:07: #1 total tags in treatment: 6197 INFO @ Fri, 05 Jul 2019 18:13:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:13:07: #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 18:13:07: #1 tags after filtering in treatment: 5755 INFO @ Fri, 05 Jul 2019 18:13:07: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 18:13:07: #1 finished! INFO @ Fri, 05 Jul 2019 18:13:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:13:07: #2 number of paired peaks: 228 WARNING @ Fri, 05 Jul 2019 18:13:07: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Fri, 05 Jul 2019 18:13:07: start model_add_line... INFO @ Fri, 05 Jul 2019 18:13:07: start X-correlation... INFO @ Fri, 05 Jul 2019 18:13:07: end of X-cor INFO @ Fri, 05 Jul 2019 18:13:07: #2 finished! INFO @ Fri, 05 Jul 2019 18:13:07: #2 predicted fragment length is 292 bps INFO @ Fri, 05 Jul 2019 18:13:07: #2 alternative fragment length(s) may be 11,55,117,153,185,229,268,292,392,442,488,568,590 bps INFO @ Fri, 05 Jul 2019 18:13:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.20_model.r INFO @ Fri, 05 Jul 2019 18:13:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:13:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:13:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:13:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:13:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:13:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585792/ERX585792.20_summits.bed INFO @ Fri, 05 Jul 2019 18:13:07: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling