BWA mem failing to locate index files

Question

[aalith]

I've seen a million forum posts about this topic, however, I still cannot figure out the issue with my command line

I indexed my reference genome (hg38... Homo_sapiens_assembly38.fasta) with bwa and samtools to create files with the same name + .fai .pac .amb .ann .bwt .dict .sa

The index files and ref genome are in the same folder

I downloaded bwa in a gatk docker image (so apt-get install bwa). My fastq file is in the home directory

Here is my command line

bwa mem -M -p -t 12 /mydata/RefGenomes/hg38/Homo_sapiens_assembly38.fasta f797.fastq > f797.sam

Error message

[E::bwa_idx_load_from_disk] fail to locate the index files

[GenoMax]

What command did you use to create the index? There was no error during that process?

[aalith]

bwa index -p Homo_sapiens_assembly38 -b 1000000000 -a bwtsw /path/to/Homo_sapiens_assembly38.fasta

I think this ran with no problem. It spit back out the 5 index types that I indicated above. I renamed each file to have the prefix "Homo_sapiens_assembly38.fasta." It also printed this..

Finished constructing BWT in 27 iterations.
[bwa_index] 2601.39 seconds elapse.
[bwa_index] Update BWT... 20.59 sec
[bwa_index] Pack forward-only FASTA... 20.92 sec
[bwa_index] Construct SA from BWT and Occ...
1083.39 sec
[main] Version: 0.7.12-r1039
[main] Real time: 3954.316 sec; CPU: 3753.260 sec

[GenoMax]

I renamed each file to have the prefix "Homo_sapiens_assembly38.fasta."

Why? You had provided a prefix name Homo_sapiens_assembly38 for your index. Just use that prefix name in your alignment. Do not change file names after running the indexing.

[aalith]

I originally didn't rename them when I ran my bwa mem command, and it still gave the same error. Should I make my .dict and .fai indices have the same name as the other 5 bwa index files?

[GenoMax]

You made the .dict and .fai files for GATK/some other software? Those should not be needed for bwa.

[aalith]

Yea, downloaded them from the GATK bundle FTP, I think.

I also tried inputting the path to the reference genome folder and indices instead of the fasta file itself. Still didn't work

[GenoMax]

After the index creation did you move any of the files around? Does the following work?

bwa mem -M -p -t 12 /full_path_to_folder_with_index_files/Homo_sapiens_assembly38  f797.fastq > f797.sam

[aalith]

I moved the index files from docker to the folder in my hard drive with the ref genome. I will try this command in a bit