Does the `--host_fasta` need to be unzipped?
Tried to launche the pipeline with a gzipped host fasta but it failed in teh DATABASES:GET_DB_VERSIONS
process with following error:
Error executing process > 'DATABASES:GET_DB_VERSIONS (1)'
Caused by:
Process `DATABASES:GET_DB_VERSIONS (1)` terminated with an error exit status (1)
Command executed:
if [[ "Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa.gz" != "" ]]
then
echo "Host_genome Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa.gz" > host_genome_db.txt
fi
if [[ "nodes.dmp" != "" ]]
then
echo "Kaiju nodes.dmp" > kaiju_db.txt
fi
if [[ "db_eggnog_mapper" != "" ]]
then
echo "Eggnog_Mapper db_eggnog_mapper" > eggnog_db.txt
fi
if [[ "new_taxdump" != "" && "prot.accession2taxid.FULL" != "" ]]
then
echo "Taxdump new_taxdump" > taxdump_db.txt
echo "Accession2taxid prot.accession2taxid.FULL" > accession_db.txt
fi
if [[ "diamond_nr_db.dmnd" != "" ]]
then
echo "Diamond diamond_nr_db.dmnd" > diamond_db.txt
fi
if [[ "release207_v2" != "" ]]
then
echo "GTDBTK release207_v2" > gtdbtk_db.txt
fi
checkm2=$(checkm2 database --current 2>&1 | awk '{ print $5 }')
echo "Diamond_checkm2 $checkm2" > checkm2_db.txt
if [[ `ls | grep db.txt` ]]
then
for i in *_db.txt
do
cat $i >> all_db.txt
done
else
touch all_db.txt
fi
db_versions.py -a all_db.txt >> db_versions.tsv
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: While bind mounting '/work:/work': destination is already in the mount point list
Traceback (most recent call last):
File "/dir/metagwgs_v2.3/bin/db_versions.py", line 48, in <module>
main()
File "/dir/metagwgs_v2.3/bin/db_versions.py", line 42, in main
list_info=info_db(line.strip())
File "/dir/metagwgs_v2.3/bin/db_versions.py", line 16, in info_db
size = f"{size} ({genome_size(path)} seq)"
File "/dir/metagwgs_v2.3/bin/db_versions.py", line 26, in genome_size
genome = txt.read()
File "/opt/conda/envs/binning/lib/python3.8/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte