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After installing StrainFLAIR as required on your github website and installing seqwish using conda, I tried to run StrainFLAIR on your minimal dataset using the command:
StrainFLAIR.sh index -i data/list_fasta_min.txt -o myproject
Unfortunately, I get the following error, although there is no problem with disk space or permissions and other dependency tools such as prodigal and cd-hit use the same /tmp directory without any problem:
After installing StrainFLAIR as required on your github website and installing seqwish using conda, I tried to run StrainFLAIR on your minimal dataset using the command:
StrainFLAIR.sh index -i data/list_fasta_min.txt -o myproject
Unfortunately, I get the following error, although there is no problem with disk space or permissions and other dependency tools such as prodigal and cd-hit use the same /tmp directory without any problem:
GRAPHS CONSTRUCTION
mkdir myproject/graphs
graphs_construction -s myproject/all_genes_extended.fasta -c myproject/clusters/all_genes_clusters.clstr -o myproject/graphs
[seqwish::tempfile]: couldn't create temp directory: /tmp/tmph647__ej/cluster_temp.work/seqwish-z7WwsM
[seqwish::tempfile]: couldn't create temp directory: /tmp/tmpiungev29/cluster_temp.work/seqwish-ZHeMAX
[seqwish::tempfile]: couldn't create temp directory: /tmp/tmpdlx6kgou/cluster_temp.work/seqwish-ko0LE2
Could you please tell me where the problem is and how to solve it?
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