samtools sort: failed to read header from "-" #11
Description
Hi, first thank you for creating this fantastic pipeline!
When I tried to run codefreq according to the docs, I got this error from samtools sort . Have you seen this issue before? Could it be related to the samtools version?
./fastq2codfreq -v -r profiles/HIV1.json -d ../test
latest: Pulling from hivdb/codfreq-runner
Digest: sha256:886cff8ae2415e11b2ac19810effb926fe1b291b50f738b082545f288fba02bf
Status: Image is up to date for hivdb/codfreq-runner:latest
docker.io/hivdb/codfreq-runner:latest
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Pre-processing /fastqfiles/./sample_test using fastp...
Done
Aligning /fastqfiles/./sample_test with HXB2_x_ConsensusB...
[W::hts_set_opt] Cannot change block size for this format
samtools sort: failed to read header from "-"
Aborted!