I am re-aligning the same .fastq files to both hg38 and CHM13 to compare the alignments. My hg38 alignment runs fine but CHM13 is getting this error:
[E::bwa_idx_load_from_disk] fail to locate the index files
/app/software/BWA/0.7.17-GCC-8.3.0/bin/bwa mem -t 4 -M -R @RG\tID:no_id\tLB:no_library\tPL:no_platform\tPU:no_unit\tSM:test /grp/reference/T2T-CHM13/RefSeq_v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.fna results/fastqs/test_fastq1.fq.gz results/fastqs/test_fastq2.fq.gz
We have tried reindexing with
bwa index GCF_009914755.1_T2T-CHM13v2.0_genomic.fna multiple times and received the same error. A colleague in a different group has reported the same issues with using BWA to align to CHM13.
I assume this is a formatting issue but I don't know what the incompatibility is. My understanding is that .fa and .fna are equivalent formats, and BWA builds a .fai from our .fna without throwing any errors. CHM13 is 3.0 GB total so the chromosomes should not be over the 2 GB limit. Any suggestions on how to trace the source of this issue?
Note: I've also submitted an issue on the BWA github page. Please let me know if there's a more appropriate forum for me to ask this!