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CSB5 / lofreq

LoFreq Star: Sensitive variant calling from sequencing data
http://csb5.github.io/lofreq/
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Permant error in the first step #134

Open beginner984 opened 1 year ago

beginner984 commented 1 year ago

Hi

What does this error means please?


fi1d18@RBGO-Server2:/data/Continuum/WES/vcf$ ./lofreq_star-2.1.0/bin/lofreq call -f resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -o vars.vcf NG-27280_CLTSS_LTS_001A_lib506241_7636_2_MarkedDup.bam
WARNING(lofreq_call.c|warn_old_fai): Index for fasta file (resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta.fai) is older than fasta file! You should reindex (using faidx)!
[fai_fetch_seq] The sequence "NC_000001.11" not found
FATAL(plp.c|mplp_func:645): Can't compute BAQ or IDAQ without reference sequence
fi1d18@RBGO-Server2:/data/Continuum/WES/vcf$

I am just certain that the reference genome in this command and for fastq file alignment was the same.

Thanks for any help

andreas-wilm commented 1 year ago

Well something is off with the reference. The index is out of date for one. Please reindex with samtools faidx. But it also seems like the reference used here and for mapping were different. You can compare what you get from samtools view -H and what you see in the .fai file.