Job ID = 2007678 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,419 reads read : 8,838 reads written : 8,838 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR467418.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: 00:00:00 4419 reads; of these: 4419 (100.00%) were paired; of these: 535 (12.11%) aligned concordantly 0 times 3539 (80.09%) aligned concordantly exactly 1 time 345 (7.81%) aligned concordantly >1 times ---- 535 pairs aligned concordantly 0 times; of these: 60 (11.21%) aligned discordantly 1 time ---- 475 pairs aligned 0 times concordantly or discordantly; of these: 950 mates make up the pairs; of these: 901 (94.84%) aligned 0 times 40 (4.21%) aligned exactly 1 time 9 (0.95%) aligned >1 times 89.81% overall alignment rate Time searching: 00:00:00 Overall time: 00:00:00 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] 4 / 3939 = 0.0010 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 16:18:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.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 16:18:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:18:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:18:03: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:18:03: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:18:03: #1 total tags in treatment: 3880 INFO @ Fri, 05 Jul 2019 16:18:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:18:03: #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 16:18:03: #1 tags after filtering in treatment: 3878 INFO @ Fri, 05 Jul 2019 16:18:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:18:03: #1 finished! INFO @ Fri, 05 Jul 2019 16:18:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:18:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:18:03: #2 number of paired peaks: 142 WARNING @ Fri, 05 Jul 2019 16:18:03: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Fri, 05 Jul 2019 16:18:03: start model_add_line... INFO @ Fri, 05 Jul 2019 16:18:03: start X-correlation... INFO @ Fri, 05 Jul 2019 16:18:03: end of X-cor INFO @ Fri, 05 Jul 2019 16:18:03: #2 finished! INFO @ Fri, 05 Jul 2019 16:18:03: #2 predicted fragment length is 295 bps INFO @ Fri, 05 Jul 2019 16:18:03: #2 alternative fragment length(s) may be 4,37,81,125,160,181,204,232,267,295,316,351,371,392,458,491,543 bps INFO @ Fri, 05 Jul 2019 16:18:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.05_model.r INFO @ Fri, 05 Jul 2019 16:18:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:18:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:18:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:18:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:18:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:18:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.05_summits.bed INFO @ Fri, 05 Jul 2019 16:18:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 16:18:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.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 16:18:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:18:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:18:04: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:18:04: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:18:04: #1 total tags in treatment: 3880 INFO @ Fri, 05 Jul 2019 16:18:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:18:04: #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 16:18:04: #1 tags after filtering in treatment: 3878 INFO @ Fri, 05 Jul 2019 16:18:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:18:04: #1 finished! INFO @ Fri, 05 Jul 2019 16:18:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:18:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:18:04: #2 number of paired peaks: 142 WARNING @ Fri, 05 Jul 2019 16:18:04: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Fri, 05 Jul 2019 16:18:04: start model_add_line... INFO @ Fri, 05 Jul 2019 16:18:04: start X-correlation... INFO @ Fri, 05 Jul 2019 16:18:04: end of X-cor INFO @ Fri, 05 Jul 2019 16:18:04: #2 finished! INFO @ Fri, 05 Jul 2019 16:18:04: #2 predicted fragment length is 295 bps INFO @ Fri, 05 Jul 2019 16:18:04: #2 alternative fragment length(s) may be 4,37,81,125,160,181,204,232,267,295,316,351,371,392,458,491,543 bps INFO @ Fri, 05 Jul 2019 16:18:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.10_model.r INFO @ Fri, 05 Jul 2019 16:18:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:18:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:18:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:18:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:18:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:18:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.10_summits.bed INFO @ Fri, 05 Jul 2019 16:18:04: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 16:18:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.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 16:18:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:18:05: #1 read treatment tags... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:18:05: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:18:05: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:18:05: #1 total tags in treatment: 3880 INFO @ Fri, 05 Jul 2019 16:18:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:18:05: #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 16:18:05: #1 tags after filtering in treatment: 3878 INFO @ Fri, 05 Jul 2019 16:18:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:18:05: #1 finished! INFO @ Fri, 05 Jul 2019 16:18:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:18:05: #2 number of paired peaks: 142 WARNING @ Fri, 05 Jul 2019 16:18:05: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Fri, 05 Jul 2019 16:18:05: start model_add_line... INFO @ Fri, 05 Jul 2019 16:18:05: start X-correlation... INFO @ Fri, 05 Jul 2019 16:18:05: end of X-cor INFO @ Fri, 05 Jul 2019 16:18:05: #2 finished! INFO @ Fri, 05 Jul 2019 16:18:05: #2 predicted fragment length is 295 bps INFO @ Fri, 05 Jul 2019 16:18:05: #2 alternative fragment length(s) may be 4,37,81,125,160,181,204,232,267,295,316,351,371,392,458,491,543 bps INFO @ Fri, 05 Jul 2019 16:18:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.20_model.r INFO @ Fri, 05 Jul 2019 16:18:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:18:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:18:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:18:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:18:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:18:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433653/ERX433653.20_summits.bed CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:18:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling