Open erah1 opened 3 months ago
I am trying to align a couple of paired-end sample fq.gz file using bwa mem, and I received the following error message.
[M::bwa_idx_load_from_disk] read 0 ALT contigs orig.samal_2.fq.gz > /path/to/genome/genome_assembly.fasta /path/to/sample\ [M::bwa_idx_load_from_disk] read 0 ALT contigs _R1.fq.gz'. open file /path/to/sample
This creates instantaneously an empty .sam file which name is sample.orig.sam, and the code stops running.
My command was: bwa mem -t 32 -M ${refGen_fasta} sample_R1.fq.gz sample_R2.fq.gz > sample_orig.sam
bwa mem -t 32 -M ${refGen_fasta} sample_R1.fq.gz sample_R2.fq.gz > sample_orig.sam
I am trying to align a couple of paired-end sample fq.gz file using bwa mem, and I received the following error message.
This creates instantaneously an empty .sam file which name is sample.orig.sam, and the code stops running.
My command was:
bwa mem -t 32 -M ${refGen_fasta} sample_R1.fq.gz sample_R2.fq.gz > sample_orig.sam