why I get "Running twoBitToFa failed" when loading chopchop

Hi everyone,

I'm working on chopchop to design sgRNAs for CRISPR/Cas9 on HPCC.

As to twoBitToFa, I could successfully use it(with path) to convert .2bit to .fasta. I tried sc, hg38 and K.p(reported). However, it turned out Running twoBitToFa failed loading chopchop. Does anyone know why and how to fix it?

I mainly followed instructions as follows.

The previous steps I took are listed in the following:

get gene_table
download .2bit file
convert .2bit to .fasta using twoBitToFa
get compressed version using bowtie build
modify config.json

enter image description here

chopchop twobittofa crispr

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updated 1.3 years ago by GenoMax

• written 1.8 years ago by WYZ1120zzh •

Did you get this fixed?

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written 1.3 years ago by Eric •

Can you clarify what step you are getting the error at and the command you are running? Original poster was not clear about that either.

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written 1.3 years ago by GenoMax

This is the command:

/chopchop_query.py \
  --genePred_file "/path/to/Zmays.gene_table" \
  -G "Zmays" \
  -o "${OUTPUT}" \
  --consensusUnion \
  --scoringMethod DOENCH_2016 \
  -t WHOLE

It fails in coordToFasta of chopchop.py when executing line 1155

./twoBitToFa -seq=Chr4 -start=234540973 -end=234541809 /path/to/crispr/2bit_folderNew/Zmays.2bit stdout 2> /path/to/output/twoBitToFa.err

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written 1.3 years ago by Eric •

My issue was I didn't have full paths in my JSON

  "PATH": {
    "PRIMER3": "/path/to/chopchop/primer3_core",
    "BOWTIE": "/path/to/chopchop/bowtie/bowtie",
    "TWOBITTOFA": "/path/to/chopchop/twoBitToFa",

I can't speak for the original poster as they had full paths. I realized when I attempted to run the ./twoBitToFa -seq=Chr4... command manually that it worked as expected. Knowing it works I updated to full path and I have past this error.

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written 1.3 years ago by Eric •

Good to know.

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written 1.3 years ago by GenoMax

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