I am trying to run phame.ctl file to construct a phylogenetic tree using .contigs files. When I run the command everything goes right, but at last an error message pups up showing error in running raxmlHPC.
[00:00:03] Checking directories and files…
[00:00:03] Complete.
[00:00:03] Preparing files…
[00:00:08] Complete.
[00:00:08] Running NUCmer on contigs
[00:08:22] Beginning SNP detection pipeline
[00:08:22] Starting with gaps
[00:08:22] Gap identification complete
[00:08:22] GFF file provided, SNPs will be differentiated as coding vs noncoding
[00:08:22] Preparing to identify SNPs
[00:10:36] SNP database complete
[00:10:36] Reconstructing all SNPs phylogeny
Uncaught exception from user code:
Error running raxmlHPC-PTHREADS -p 10 -T 2 -m GTRGAMMAI -s /mnt/lustre/koa/scratch/pdahal/ceti/workdir/results/bceti_all_snp_alignment.fna -w /mnt/lustre/koa/scratch/pdahal/ceti/workdir/results -n bceti_all 2>>/mnt/lustre/koa/scratch/pdahal/ceti/workdir/results/bceti.error >> /mnt/lustre/koa/scratch/pdahal/ceti/workdir/results/bceti.log
I am new in this field and I have no clue how to fix this. Can anyone help me identifying the problem?