bc unknown command

[thdurand4]

Hello i am trying to use goldrush assembler on my diploid genome of mosquito and when i launch the pipeline every works fine but for one step when it launch : goldrush-edit-ntedit script i have an error because he doesn"t know the bc commande i think its at this line :

size_diff=$(echo "scale=4; $output_size / $input_size" | bc).

But it is very strange because when i am on my terminal i can use bc command but when i launch the pipeline, after he fails i can't use anymore bc command.

I have installed it well with conda/mamba.

Thanks for your answers. Théo

[lcoombe]

Hi Théo,

That is quite strange! What version of goldrush are you using, and what conda build? (You can find that with conda list) If you run which bc, what path do you see?

Also, could you share your full command and standard out/error with us?

Thank you for your interest in GoldRush! Lauren

[thdurand4]

Hello

When i use conda list command i see this :

goldrush 1.0.3 py38h2494328_1 bioconda

which bc : /usr/bin/bc

[thdurand4]

Ohhhhh i think i got it,

I use a cluster to launch Goldrush and i just saw when i am on a node bc command doesn't exist but when i am on master its work that strange !

I will try to fix it.

[lcoombe]

Ok great! Yeah, was asking about the version because I only added bc as a conda dependency in the build 1.0.1_1 - so if you're using GoldRush on a node without bc installed using that updated conda recipe should also fix it!