Open Rahimlou opened 1 year ago
I have the exact same error. Any updates?
Are u using conda?
if the script was not found is because trinity cannot be located. The insilico normalization step is done using trinity scripts.
cheers
Sergio
Thanks for the prompt response. Yes, using conda. Do I have to install trinity separately then?
Not really...
the pipeline runs but breaks at normalization, correct?
Sergio
Not really...
the pipeline runs but breaks at normalization, correct?
Sergio
Yes, that is correct.
I'm getting the following error message while running the full analysis.
Error executing process > 'normalize_reads (control_R)'
Caused by: Process
normalize_reads (control_R)
terminated with an error exit status (127)Command executed:
echo control_R
echo -e "\n-- Starting Normalization --\n"
mem=$( echo 150 GB | cut -f 1 -d " " )
insilico_read_normalization.pl --seqType fq -JM ${mem}G --max_cov 100 --min_cov 1 --left left-control_R.filter.fq --right right-control_R.filter.fq --pairs_together --PARALLEL_STATS --CPU 15
echo -e "\n-- DONE with Normalization --\n"
cat .command.out | grep "stats_file" -A 3 | tail -n 3 >control_R_normStats.txt
cp left.norm.fq left-"control_R".norm.fq cp right.norm.fq right-"control_R".norm.fq
rm $(readlink -e left.norm.fq) $(readlink -e right.norm.fq ) left.norm.fq right.norm.fq
Command exit status: 127
Command output: control_R
-- Starting Normalization --
Command error: control_R
-- Starting Normalization --
.command.sh: line 8: insilico_read_normalization.pl: command not found