Error during annotation with prokka
Dear,
When I run the analysis step, it fails and gives the following error:
Provided cores: 1 Rules claiming more threads will be scaled down. Job counts: count jobs 1 ANALYSIS 1 PLATYPUS 1 annotate 1 assembly_contig_length 1 call_contig_depth 1 call_gene_depth 1 fastqc_preprocessed 1 fastqc_raw 1 krona 1 metaquast 1 reads_count 1 rename_stat_output 1 variant_calling 1 visualize 1 vizbin 15
rule annotate: input: Assembly/mt.assembly.merged.fa output: Analysis/annotation/annotation.filt.gff, Analysis/annotation/prokka.faa, Analysis/annotation/prokka.fna, Analysis/annotation/prokka.ffn, Analysis/annotation/prokka.fsa jobid: 16
prokka --force --outdir Analysis/annotation --prefix prokka --cpus 24 --metagenome Assembly/mt.assembly.merged.fa >> Analysis/annotation.log 2>&1
# Prokka gives a gff file with a long header and with all the contigs at the bottom. The command below removes the
# And keeps only the gff table.
LN=`grep -Hn "^>" Analysis/annotation/prokka.gff | head -n1 | cut -f2 -d ":" || if [[ $? -eq 141 ]]; then true; else exit $?; fi`
LN1=1
LN=$(($LN-$LN1))
head -n $LN Analysis/annotation/prokka.gff | grep -v "^#" | sort | uniq | grep -v "^==" > Analysis/annotation/annotation.filt.gff
Error in job annotate while creating output files Analysis/annotation/annotation.filt.gff, Analysis/annotation/prokka.faa, Analysis/annotation/prokka.fna, Analysis/annotation/prokka.ffn, Analysis/annotation/prokka.fsa. RuleException: CalledProcessError in line 11 of /scratch/gencore/ma5877_test_software/meta_trans/imp/IMP/rules/Analysis/prokka.rule: Command ' prokka --force --outdir Analysis/annotation --prefix prokka --cpus 24 --metagenome Assembly/mt.assembly.merged.fa >> Analysis/annotation.log 2>&1
# Prokka gives a gff file with a long header and with all the contigs at the bottom. The command below removes the
# And keeps only the gff table.
LN=`grep -Hn "^>" Analysis/annotation/prokka.gff | head -n1 | cut -f2 -d ":" || if [[ $? -eq 141 ]]; then true; else exit $?; fi`
LN1=1
LN=$(($LN-$LN1))
head -n $LN Analysis/annotation/prokka.gff | grep -v "^#" | sort | uniq | grep -v "^==" > Analysis/annotation/annotation.filt.gff
' returned non-zero exit status 2
File "/scratch/gencore/ma5877_test_software/meta_trans/imp/IMP/rules/Analysis/prokka.rule", line 11, in __rule_annotate File "/scratch/gencore/conda3/envs/imp_env/lib/python3.5/concurrent/futures/thread.py", line 55, in run Will exit after finishing currently running jobs. Exiting because a job execution failed. Look above for error message
And when I looked at the "annotation.log" file it shows the following error:
Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module) (@INC contains: /scratch/gencore/software/MOCAT/src /scratch/gencore/conda3/envs/imp_env/lib/site_perl/5.26.2/x86_64-linux-thread-multi /scr atch/gencore/conda3/envs/imp_env/lib/site_perl/5.26.2 /scratch/gencore/conda3/envs/imp_env/lib/5.26.2/x86_64-linux-thread-multi /scratch/gencore/conda3/envs/imp_env/lib/5.26.2 .) at /scratch/gencore/conda3/envs/imp_env/bin/prokka line 29
Please help me to fix this issue.
Thanks