Coordinates must be > 0

[carolinapinapaez]

I've started a run of graphtyper 2.7.2 with a command for a chromosome of my reference:

graphtyper genotype reference.fasta --sams=$BAMLIST --sams_index=$BAILIST --region=Chr5_A_fumigatus_Af293 --threads=16 --verbose --avg_cov_by_readlen=$BAMCOV --output=test

[[2023-11-16 16:15:47.364] Running the 'genotype' subcommand.
[2023-11-16 16:15:47.382] Genotyping region Chr5_A_fumigatus_Af293:1-50000
[2023-11-16 16:15:47.382] Path to genome is '/bigdata/stajichlab/shared/projects/Population_Genomics/Afumigatus_Global/genome/FungiDB-50_AfumigatusAf293_Genome.fasta'
[2023-11-16 16:15:47.382] Running with up to 16 threads.
[2023-11-16 16:15:47.382] Input contains 10 BAM/CRAM files.
[2023-11-16 16:15:47.383] Temporary folder is /scratch/carolinp/1023875/graphtyper_231116_161547_Chr5_A_fumigatus_Af293_000000001.AdTuVX
[2023-11-16 16:15:49.772] Running bamShrink, which copies read data to temporary disk.
[E::hts_parse_region] Coordinates must be > 0
[2023-11-16 16:15:49.802] bamshrink.cpp:692 Could not set region to Chr5_A_fumigatus_Af293:1-50101 when using index /bigdata/stajichlab/shared/projects/Population_Genomics/Afumigatus_Global/aln/CM2730.cram.crai

I've used these.bam and .bai files for other purposes with no issues.

[hannespetur]

Hey,

can you confirm that you can read the region using samtools?

samtools view /bigdata/stajichlab/shared/projects/Population_Genomics/Afumigatus_Global/aln/CM2730.cram Chr5_A_fumigatus_Af293:1-50101 | less -S

Best,
Hannes