ERROR: Command samtools sort returned non-zero exit status -6

[mabouaassi]

I am getting an error with the Samtools sort command step when running TETyper on my metagenomic assembled genome. I ran TETyper on your test file and got the same error. Any advice? ~Marlene

$ TETyper.py --ref ~/TETyper-master/IS26.fasta --fq1 ~/TETyper-master/SRR1582895_sm_1.fq.gz --fq2 ~/TETyper-master/SRR1582895_sm_2.fq.gz --outprefix test --flank_len 5
INFO: TETyper version 1.1
INFO: TETyper command: ~/scripts/miniconda/bin/TETyper.py --ref ~/TETyper-master/IS26.fasta --fq1 ~/TETyper-master/SRR1582895_sm_1.fq.gz --fq2 ~/TETyper-master/SRR1582895_sm_2.fq.gz --outprefix test --flank_len 5
INFO: Successfully read in reference of length 820
INFO: Blast database not found. Creating database automatically.
INFO: Bwa index files not found. Creating index automatically.
ERROR: Command samtools sort returned non-zero exit status -6

[csernab]

I had the same problem on a Mac OSX 12.3.1.
This works for me:
https://github.com/conda/conda/issues/8103#issuecomment-739312493

conda install -c bioconda samtools=1.9

I hope you find it helpful!