Closed george-githinji closed 8 years ago
Can you let me know which version of IVA you are running (iva --version)? I can't reproduce this error. Could you also paste the entire terminal output?
Does iva --test out_dir work for you?
Thanks, Martin
I am running IVA version 1.0.3 as part of a SLURM batch script. This is what I get in my error file.
usage: iva [options] {-f reads_fwd -r reads_rev | --fr reads} <output directory>
iva: error: unrecognized arguments: assemblies/iva/9465_1#13
This is how I call it from my batch script.
if [[ $ASSEMBLER == "iva" ]]; then
module load iva/1.0.3
echo "de novo assembly with IVA"
mkdir -p "$OUTPUT_DIR/$ASSEMBLER"
iva --threads "$THREADS" --verbose 2 -f "$FORWARD" -r "$REVERSE" "$OUTPUT_DIR/$ASSEMBLER/$SAMPLENAME"
I ran iva --test out_dir
and it works.
my module environment has all the dependencies
Currently Loaded Modulefiles:
1) python/3.5.0 3) MUMmer/3.23 5) samtools/1.2 7) perl/5.22.0 9) bioperl/1.6.923
2) kmc/2.1.1 4) smalt/0.7.6 6) trimmomatic/0.33 8) kraken/kraken-0.10.5-beta 10) iva/qc
If you want double verbosity, use -v -v (ie not -v 2). It's interpreting the 2 as the name of the output directory and getting confused. Try this:
iva --threads 10 -v -v -f forward_reads.gz -r reverse_reads.gz output_directory
Martin
Thank you Martin.
I am running into this error while using IVA.
IVA: error: unrecognized arguments: path_to_output_directory
the commandline arguments are
iva --threads 10 --verbose 2 -f forward_reads.gz -r reverse_reads.gz output_directory