"Could not locate a Bowtie index corresponding to basename "refdir/barcodes-ref"

[jmath97]

Hi,

I'm processing two fastq files through the Du Novo pipeline. I planned to proceed as suggested by the processing steps posted in the github page. At the 'optional' error correction step, the program produces an error:

"Could not locate a Bowtie index corresponding to basename "refdir/barcodes-ref".
Command: bowtie-align --wrapper basic-0 --chunkmbs 512 --threads 1 -f --sam -a --best -v 3 refdir/barcodes-ref refdir/barcodes.fa /rugpfs/fs0/marr_lab/store/jmathai/WTminus/Analysis_dunovo/barcodes.sam

I've provided the script details below. If you could clarify why this error is occurring, that would be greatly appreciated!

Thanks!

SCRIPT:

conda activate dunovo

DUNOVO_HOME="/rugpfs/fs0/marr_lab/store/jmathai/softwares/miniconda/envs/dunovo/dunovo"
RAW_DATA="/rugpfs/fs0/marr_lab/store/jmathai/WTminus"
WORKING_DIR="/rugpfs/fs0/marr_lab/store/jmathai/WTminus/Analysis_dunovo"

cd $WORKING_DIR
pwd

## Sort the reads into families based on their barcodes and split the barcodes from the sequence
$DUNOVO_HOME/make-families.sh $RAW_DATA/WTminus_R1.fastq $RAW_DATA/WTminus_R2.fastq > families.tsv
echo "[CMD] make-families.sh $RAW_DATA/WTminus_R1.fastq $RAW_DATA/WTminus_R2.fastq > families.tsv"

## Correct errors in barcodes
$DUNOVO_HOME/baralign.sh families.tsv refdir $WORKING_DIR/barcodes.sam
echo "[CMD] baralign.sh families.tsv refdir barcodes.sam"

$DUNOVO_HOME/correct.py families.tsv refdir/barcodes.fa barcodes.sam | sort > families.corrected.tsv
echo "[CMD] correct.py families.tsv refdir/barcodes.fa barcodes.sam | sort > families.corrected.tsv"

[NickSto]

Thanks for the report! Could you check which version of Du Novo you're running? A quick correct.py --version should tell you.