Hi! I'm new in this world and I need help to understand how to overcome the problem that I have. I used bwa mem for the alignment of a sample with hg38 reference genome and got this error, can't really understand why. The code that I'm running is this one:
bwa mem \ /home/arturo/Documenti/hg38.fa /home/arturo/Documenti/PATIENT/PATIENT_TRIMMED/PATIENT-BM_S7_L001_R1_001_trimmed.fastq.gz \ /home/arturo/Documenti/PATIENT/PATIENT_TRIMMED/PATIENT-BM_S7_L001_R2_001_trimmed.fastq.gz | \ samtools view -bS - > /home/arturo/Documenti/PATIENT/PATIENT_BAM/PATIENT_BM_unsorted.bam
The output is:
[E::bwa_idx_load_from_disk] fail to locate the index files [main_samview] fail to read the header from "-".
What could be wrong here?
I have also another question: the hg38 reference genome should be unzipped once downloaded or not?
Please use for reference input fasta no .amb:
Not to use
Le me know if it works.
First of all Thank you for the answer! I have already created the BWA index of my FASTA file which are the same as you listed above (i think you were ment to write amb instead of amp). I've tried to run the code also with those files but still getting the same error.
[main_samview] fail to read the header from "-"
Could also be a problem of where my BWA index files are? I have it in the same directory of the hg38 FASTA file