Entering edit mode
5.4 years ago
aalith
▴
20
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
What command did you use to create the index? There was no error during that process?
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..
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.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?
You made the
.dict
and.fai
files for GATK/some other software? Those should not be needed forbwa
.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
After the index creation did you move any of the files around? Does the following work?
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