error running get_repeat_coords.pl

[pdimens]

Hello, I have installed phame using the first conda installation method, and I see that in the produced ____.error file there are several errors.

1. error running get_repeat_coords.pl -l 75 -i 97 -o path/to/dir
2. error running nucmer_command1 nucmeer --maxmatch -p prefix fna1 fna2
   I'm unfamiliar with troubleshooting phame, but these errors don't provide enough information for me to find the route cause. Below is the full error log

➜ cat tunas.error 
Smartmatch is experimental at /home/pdimens/micromamba/envs/phylogeny/bin/../lib/misc_funcs.pm line 26.
nucmer --maxmatch --nosimplify --prefix=seq_seq229226 /home/pdimens/tuna_phylogeny/workdir/files/yellowfin.fna /home/pdimens/tuna_phylogeny/workdir/files/yellowfin.fna 2>/dev/null at /home/pdimens/micromamba/envs/phylogeny/bin/get_repeat_coords.pl line 44.
Error running get_repeat_coords.pl -l 75 -i 97 -o /home/pdimens/tuna_phylogeny/workdir/results/yellowfin_repeat_coords.txt -s /home/pdimens/tuna_phylogeny/workdir/results/yellowfin_repeat_stats.txt /home/pdimens/tuna_phylogeny/workdir/files/yellowfin.fna.
nucmer --maxmatch --nosimplify --prefix=seq_seq229224 /home/pdimens/tuna_phylogeny/workdir/files/pacificbluefin.fna /home/pdimens/tuna_phylogeny/workdir/files/pacificbluefin.fna 2>/dev/null at /home/pdimens/micromamba/envs/phylogeny/bin/get_repeat_coords.pl line 44.
Error running get_repeat_coords.pl -l 75 -i 97 -o /home/pdimens/tuna_phylogeny/workdir/results/pacificbluefin_repeat_coords.txt -s /home/pdimens/tuna_phylogeny/workdir/results/pacificbluefin_repeat_stats.txt /home/pdimens/tuna_phylogeny/workdir/files/pacificbluefin.fna.
nucmer --maxmatch --nosimplify --prefix=seq_seq229225 /home/pdimens/tuna_phylogeny/workdir/files/southernbluefin.fna /home/pdimens/tuna_phylogeny/workdir/files/southernbluefin.fna 2>/dev/null at /home/pdimens/micromamba/envs/phylogeny/bin/get_repeat_coords.pl line 44.
Error running get_repeat_coords.pl -l 75 -i 97 -o /home/pdimens/tuna_phylogeny/workdir/results/southernbluefin_repeat_coords.txt -s /home/pdimens/tuna_phylogeny/workdir/results/southernbluefin_repeat_stats.txt /home/pdimens/tuna_phylogeny/workdir/files/southernbluefin.fna.
Error running nucmer_command1 nucmer --maxmatch  -p southernbluefin_southernbluefin /home/pdimens/tuna_phylogeny/workdir/results/southernbluefin_norepeats.fna /home/pdimens/tuna_phylogeny/workdir/results/southernbluefin_norepeats.fna  2>/dev/null.
Error running nucmer_command1 nucmer --maxmatch  -p southernbluefin_yellowfin /home/pdimens/tuna_phylogeny/workdir/results/southernbluefin_norepeats.fna /home/pdimens/tuna_phylogeny/workdir/results/yellowfin_norepeats.fna  2>/dev/null.
Error running nucmer_command1 nucmer --maxmatch  -p southernbluefin_pacificbluefin /home/pdimens/tuna_phylogeny/workdir/results/southernbluefin_norepeats.fna /home/pdimens/tuna_phylogeny/workdir/results/pacificbluefin_norepeats.fna  2>/dev/null.
cat: '/home/pdimens/tuna_phylogeny/workdir/results/*_repeat_stats.txt': No such file or directory
mv: cannot stat '/home/pdimens/tuna_phylogeny/workdir/results/*.snps': No such file or directory
mv: cannot stat '/home/pdimens/tuna_phylogeny/workdir/results/*.gaps': No such file or directory
mv: cannot stat '/home/pdimens/tuna_phylogeny/workdir/results/*_coords.txt': No such file or directory
mv: cannot stat '/home/pdimens/tuna_phylogeny/workdir/results/*.coords': No such file or directory
mv: cannot stat '/home/pdimens/tuna_phylogeny/workdir/results/*norepeats.fna': No such file or directory
Error running nucmer --maxmatch -b 200 -c 65 -d 0.12 -g 90 -l 20  -p southernbluefin_easternlittletuna_contig /home/pdimens/tuna_phylogeny/workdir/files/southernbluefin.fna /home/pdimens/tuna_phylogeny/workdir/files/easternlittletuna_contig.fna  2>/dev/null.

my config/control file, if it may help, looks like this

   refdir = genomes  # directory where reference (Complete) files are located
  workdir = /home/pdimens/tuna_phylogeny/workdir # directory where contigs/reads files are located and output is stored

reference = 2 # 0:pick a random reference from refdir; 1:use given reference; 2: use ANI based reference
  reffile = southernbluefin.fasta  # reference filename when option 1 is chosen

  project = tunas  # main alignment file name

  cdsSNPS = 0  # 0:no cds SNPS; 1:cds SNPs, divides SNPs into coding and non-coding sequences, gff file is required

  buildSNPdb = 0 # 0: only align to reference 1: build SNP database of all complete genomes from refdir

FirstTime = 1  # 1:yes; 2:update existing SNP alignment, only works when buildSNPdb is used first time to build DB

     data = 3  # *See below 0:only complete(F); 1:only contig(C); 2:only reads(R);
               # 3:combination F+C; 4:combination F+R; 5:combination C+R;
               # 6:combination F+C+R; 7:realignment  *See below
    reads = 2  # 1: single reads; 2: paired reads; 3: both types present;

     tree = 2  # 0:no tree; 1:use FastTree; 2:use RAxML; 3:use both;
bootstrap = 1  # 0:no; 1:yes;  # Run bootstrapping  *See below
        N = 100  # Number of bootstraps to run *See below

PosSelect = 0  # 0:No; 1:use PAML; 2:use HyPhy; 3:use both # these analysis need gff file to parse genomes to genes

     code = 2  # 0:Bacteria; 1:Virus; 2: Eukarya # Bacteria and Virus sets ploidy to haploid

    clean = 0  # 0:no clean; 1:clean # remove intermediate and temp files after analysis is complete

  threads = 25  # Number of threads to use

   cutoff = 0.1  # Linear alignment (LA) coverage against reference - ignores SNPs from organism that have lower cutoff.

   * When using data option 1,2,5 need a complete reference to align/map to.
   * Use data option 7 when need to extract SNPs using a sublist of already aligned genomes.