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Illumina / Cyrius

A tool to genotype CYP2D6 with WGS data
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ValueError: invalid contig `22` #24

Closed Giuseppe1995 closed 2 years ago

Giuseppe1995 commented 2 years ago

Hi, I am trying to run star_caller.py exactly ad described in the manual, and I am getting this error messages:

INFO:root:Processing sample I-07-1524.normal.finalSorted at 2022-03-02 11:23:54.857425 Traceback (most recent call last): File "star_caller.py", line 562, in main() File "star_caller.py", line 529, in main cyp2d6_call = d6_star_caller( File "star_caller.py", line 175, in d6_star_caller normalized_depth = get_normed_depth( File "/srv/ngs/analysis/dalteriog/Tools/Cyrius-1.1.1/depth_calling/bin_count.py", line 39, in get_normed_depth counts_for_normalization, gc_for_normalization, region_type_cn, read_length = count_reads_and_prepare_for_normalization( File "/srv/ngs/analysis/dalteriog/Tools/Cyrius-1.1.1/depth_calling/bin_count.py", line 187, in count_reads_and_prepare_for_normalization region_reads = get_read_count(bamfile, region) File "/srv/ngs/analysis/dalteriog/Tools/Cyrius-1.1.1/depth_calling/bin_count.py", line 103, in get_read_count reads = bamfile.fetch(region[0], region[1], region[2]) File "pysam/libcalignmentfile.pyx", line 1091, in pysam.libcalignmentfile.AlignmentFile.fetch File "pysam/libchtslib.pyx", line 685, in pysam.libchtslib.HTSFile.parse_region ValueError: invalid contig 22.

I am not a python expert, but I think that the error stands, maybe, in the contigs nomenclature. Nevertheless, this is quite odd because all the bam files specified in the MANIFEST_FILE have the following contings nomenclature:

chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr2 chr20 chr21 chr22 chr3 chr4

chr5 chr6 chr7 chr8 chr9 chrM chrX chrY

I don't either think that the problem is the dependencies, as I checked in this issue that I have installed all the packages with at least the version indicated (for some packages I have newer version, but I don't think this should be a problem). For a matter of completeness, here is the MANIFEST_FILE, where each line specifies a bam full path manifestBampath.txt

thank you so much in advantage Giuseppe

xiao-chen-xc commented 2 years ago

Hi @Giuseppe1995 I would guess that you specified the wrong genome in the command. Do you know if your bams are aligned against hg38 or hg19? Based on how your chromosomes are named, it's not GRCh37, but you probably used --genome 37 so that's why there was the error.

Giuseppe1995 commented 2 years ago

thank you, this solved my doubt. Thank you again