I have four total fastq files (two bulks, with forward and reverse reads for each) containing Illumina reads which I am trying to align to a reference file. The reference file has file extension ".pa" but when the script fails, the error that is returned shows that the algorithm is looking for and failing to find that same file, but with extension ".pac".
Looking around on this site, I can tell that .pac files are index files that BWA creates and uses internally. So then why would it lose track of, or fail to create, this file? What kinds of things should I do to ensure that my files are appropriate for this function call? I already ran them through fastqc and read quality looks fine.
This is being conducted on a remote server via SSH, so read/write permission issues are possible, but the error log should be documenting such things if so, and it is not. A colleague has performed alignment using the same reference genome kept at the same directory, with fewer permissions, and my script is modeled closely after his, so I can only think there must be some issue with my inputs.
Below is the function call with variable names slightly anonymized:
time bwa mem -t 8 /work/lab/reference_genomes/ref_v2.fa /scratch/user/qtlSeq/eReadsForward.fastq.gz /scratch/user/qtlSeq/eReadsReverse.fastq.gz > eAligned.sam
And the error:
[bns_restore_core] fail to open file '/work/lab/reference_genomes/ref_v2.fa.pac' : No such file or directory
General advice about how to interpret this error would be appreciated.