samtools faidx error

Question

[rbronste]

Hi trying to run an ATAC-seq pipeline and getting the following error for the above code, does anyone know if older versions of faidx had the -x flag? Thanks.

Original code:

## extract fasta per chromosome
cd ${DATA_DIR}/$GENOME
mkdir -p seq
cd seq
rm -f ${REF_FA_PREFIX}
ln -s ../${REF_FA_PREFIX} ${REF_FA_PREFIX}
samtools faidx -x ${REF_FA_PREFIX}
cp --remove-destination *.fai ../
2017-08-03 11:52:54 (167 MB/s) - “mm10_dnase_avg_fseq_signal_metadata.txt” saved [1251/1251]

Error:

    Extracting/processing data files...
    faidx: invalid option -- 'x'

    Usage:   samtools faidx <file.fa|file.fa.gz> [<reg> [...]]

Answer 1

[Matt Shirley]

I think you've modified the code a bit. The git repository has something a bit different:

## extract fasta per chromosome
cd ${DATA_DIR}/$GENOME
mkdir -p seq
cd seq
rm -f ${REF_FA_PREFIX}
ln -s ../${REF_FA_PREFIX} ${REF_FA_PREFIX}
faidx -x ${REF_FA_PREFIX}
cp --remove-destination *.fai ../

The faidx command is included as part of the pyfaidx python module, and indeed has an -x flag, which splits the input fasta into individual fasta files. That's what "extract fasta per chromosome" means in the comment.

You can install pyfaidx using pip: pip install pyfaidx

Answer 2

[h.mon]

The error message is very clear and gives the solution:

samtools faidx ${REF_FA_PREFIX}

[rbronste]

Right, just not sure why the original code had the -x, was trying to figure that out. Thanks.

[st.ph.n]

Where is the original from?

[rbronste]

https://github.com/kundajelab/atac_dnase_pipelines/blob/master/install_genome_data.sh

Line 185.

I also had to add samtools preceding faidx but thats just our samtools I guess.

[Matt Shirley]

No, it's a separate script called faidx from the pyfaidx package.

[rbronste]

Now the install_genome_data.sh has passed the error step after elimination of -x, was just confusing because the first time I ran a different version a few weeks back it had the -x and didn't stall.

Answer 3

[sonark]

Instead of using samtools to create index file, you can use IGV; under Tools -> Run igvtools... then select Index and your genome fasta file or BAM file as the input. This will give you the .fai or .bai index file.