line 8: insilico_read_normalization.pl: command not found

[Rahimlou]

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

[ntsotakos]

I have the exact same error. Any updates?

[sevragorgia]

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

[ntsotakos]

Thanks for the prompt response. Yes, using conda. Do I have to install trinity separately then?

[sevragorgia]

Not really...

the pipeline runs but breaks at normalization, correct?

Sergio

[ntsotakos]

Not really...

the pipeline runs but breaks at normalization, correct?

Sergio

Yes, that is correct.