DATABASES:GET_DB_VERSIONS error
Hi, I try to use your amazing workflow but some error appends. I work with 2x150bp illumina reads on local cluster.
my slurm script is :
#!/bin/bash
#Submit this script with: sbatch thefilename
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --cpus-per-task=60 # number of CPU per task #4
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem=464G # memory per Nodes #38
#SBATCH -J "SR" # job name
#SBATCH --mail-user=carole.belliardo@inrae.fr # email address
#SBATCH --mail-type=ALL
#SBATCH -e slurm-SR-%j.err
#SBATCH -o slurm-SR-%j.out
#SBATCH -p all
# LOAD MODULES, INSERT CODE, AND RUN YOUR PROGRAMS HERE
module load singularity/3.5.3
module load nextflow/21.04.1
cd '/kwak/hub/25_cbelliardo/25_MISTIC/tools'
nextflow run -profile singularity metagwgs/main.nf \
--skip_host_filter \
--type 'SR' \
--quality_type "illumina" \
--adapter1 "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA" \
--adapter2 "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT" \
--kaiju_db \
--diamond_bank "/database/hub/NR/NR_diamond/NR_2020_01_diamond.dmnd" \
--gtdbtk_bank "/database/hub/GTDB/release20211115/" \
--eggnogmapper_db_download \
--input "/kwak/hub/25_cbelliardo/25_MISTIC/LRvsSR/list_wgstool.csv"
On the end of the slurm output file is :
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 [[ "" != "" ]]
then
echo "Host_genome " > 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.tar.gz" != "" && "prot.accession2taxid.FULL.gz" != "" ]]
then
echo "Taxdump new_taxdump.tar.gz" > taxdump_db.txt
echo "Accession2taxid prot.accession2taxid.FULL.gz" > accession_db.txt
fi
if [[ "NR_2020_01_diamond.dmnd" != "" ]]
then
echo "Diamond NR_2020_01_diamond.dmnd" > diamond_db.txt
fi
if [[ "release20211115" != "" ]]
then
echo "GTDBTK release20211115" > gtdbtk_db.txt
fi
checkm2=$(checkm2 database --current 2>&1 | tail -n1 |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:
du: cannot access 'compiled': No such file or directory
Traceback (most recent call last):
File "/kwak/hub/25_cbelliardo/25_MISTIC/tools/metagwgs/bin/db_versions.py", line 58, in <module>
main()
File "/kwak/hub/25_cbelliardo/25_MISTIC/tools/metagwgs/bin/db_versions.py", line 52, in main
list_info=info_db(line.strip())
File "/kwak/hub/25_cbelliardo/25_MISTIC/tools/metagwgs/bin/db_versions.py", line 17, in info_db
size = process.stdout.split()[0].decode('utf-8')
IndexError: list index out of range
Work dir:
/kwak/hub/25_cbelliardo/25_MISTIC/tools/work/30/a1628d2775edb56e956e6a79cda325
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
I hope you could help me. Best regards, Carole