tamsen
commented
4 years ago Hi,
Sorry for the late response.
So, the contigs in your genome size .xml file are just numbers, as in "1" , see below: fileName="Homo_sapiens.GRCh38.dna.primary_assembly.fa" contigName="1"
And the contigs named in your bed file have chr appended, as in "chr1" , see below. chr1 762420 762565 ref|LINC00115,ref|NR_024321,ens|ENST00000473798,ens|ENST00000536430,mRNA|KJ901126,mRNA|BC017762,mRNA|AK026292
So, Pisces thinks you are looking for something in the interval chr1, and can't find such a contig in your genome. It can't fine any contig you asked for. So that's why it completes quickly.
Removing all the prepended "chr" from your bed file might do the trick, if everything else is consistent.
best Tamsen
Hello,
I installed Pisces recently to find some SNVs in my tumor-only whole exome data. I used your CreateGenomeSizeFile_5.2.9.122.tar.gz tool to get the genomesize.xml for my reference genome (Homo sapiens (GRCh38.p7). I have a feeling it might not have worked out for me. I get an output in less than a second with this message:
12/9/19 9:08 PM 1 * Starting ** 12/9/19 9:08 PM 1 Version: 5.2.10.49. 12/9/19 9:08 PM 1 Command-line arguments: . 12/9/19 9:08 PM 1 "-b /home/jlee110/Documents/octopus/3642_B5_Tum_DNA.marked.fixed.bam -callmnvs false -gvcf false -i /home/jlee110/Downloads/pisces-conda/interval/S04380110_Covered.txt -g /home/jlee110/Documents/octopus/updated_reference -o /home/jlee110/Downloads/pisces-conda -rmxnfilter 5,9,0.35". 12/9/19 9:08 PM 1 Processing genome '/home/jlee110/Documents/octopus/updated_reference' with 12 threads. 12/9/19 9:08 PM 1 Total execution time is 0.0285979s. 12/9/19 9:08 PM 1 **** Ending *****
Time: 00:00:00.9
Options helper: Setting LowDepthFilter = MinimumCoverage Options helper: Setting MinimumFrequencyFilter to MinimumFrequency Options helper: Setting TargetLODFrequency to MinimumFrequencyFilter
Pisces Copyright (c) Illumina 2019 https://github.com/Illumina/Pisces 5.2.10.49
Any help would be greatly appreciated.
GenomeSize.xml.zip
P.S. I've attached the genomesize.xml. I'm not sure if I did it correctly.
P.S.2 My interval file looks like this: chr1 65509 65625 - chr1 65831 65973 - chr1 69481 69600 ref|OR4F5,ref|NM_001005484,ens|ENST00000335137,ccds|CCDS30547.1 chr1 721381 721519 ens|ENST00000591440,ens|ENST00000591702,ens|ENST00000586288,ens|ENST00000587530,ens|ENST00000586928,ens|ENST00000589531,ens|ENST00000593022,ens|ENST00000590848,ens|ENST00000585745,ens|ENST00000588951,ens|ENST00000585768,ens|ENST00000429505,ens|ENST00000358533,mRNA|AK290103,mRNA|AK125248 chr1 721530 721806 ens|ENST00000591440,ens|ENST00000591702,ens|ENST00000586288,ens|ENST00000587530,ens|ENST00000586928,ens|ENST00000589531,ens|ENST00000593022,ens|ENST00000590848,ens|ENST00000585745,ens|ENST00000588951,ens|ENST00000585768,ens|ENST00000429505,ens|ENST00000358533,mRNA|AK290103,mRNA|AK125248 chr1 721851 721942 ens|ENST00000591440,ens|ENST00000591702,ens|ENST00000586288,ens|ENST00000587530,ens|ENST00000586928,ens|ENST00000589531,ens|ENST00000593022,ens|ENST00000590848,ens|ENST00000585745,ens|ENST00000588951,ens|ENST00000585768,ens|ENST00000429505,ens|ENST00000358533,mRNA|AK290103,mRNA|AK125248 chr1 752916 753035 ref|FAM87B,ref|NR_103536,ens|ENST00000326734,ens|ENST00000435300,mRNA|AK097327 chr1 762095 762275 ref|LINC00115,ref|NR_024321,ens|ENST00000473798,ens|ENST00000536430,mRNA|KJ901126,mRNA|BC017762,mRNA|AK026292 chr1 762280 762414 ref|LINC00115,ref|NR_024321,ens|ENST00000473798,ens|ENST00000536430,mRNA|KJ901126,mRNA|BC017762,mRNA|AK026292 chr1 762420 762565 ref|LINC00115,ref|NR_024321,ens|ENST00000473798,ens|ENST00000536430,mRNA|KJ901126,mRNA|BC017762,mRNA|AK026292
It's Agilent SureSelect V5, I just edited the extension from .bed to .txt. I used the covered.bed from Agilent's website. Bedfile I used: https://drive.google.com/file/d/1fIDOFMJbiecuKNjO5ja030mxDvEIcFCY/view