Unable to index (error with snakemake)

[AyushSaxena]

Hello,

I have been unable to get even the dry run working for me. I have been informed by our cluster support (at the University of Florida) that the installation may have had glitches. In that light, the script I'm running is the following - module load smrtsv2

${SMRT_DIR}/smrtsv.py \ --tempdir ${TMP} \ --dryrun \ --verbose \ run \ --batches 8 \ --threads 8 \ --species C.elegans \ --asm-polish arrow \ --min-support 3 \ --min-hardstop-support 3 \ ${reference} \ ${path_to_fasta}

The less verbose version of the error I'm getting is - snakemake: error: unrecognized arguments: -T Failed to index reference

I'm attaching the full (verbose) error report. Is this a problem with the installation, or am I using it wrong?

Thank you Ayush smrtsv2_32818810.txt

[paudano]

There are two problems here.

1) I think you must have an old version of SMRT-SV. The -T option was removed a while ago. Newer versions of Snakemake no longer need it (it does timestamps by default now, which is what -T used to turn on).

2) Run the shell script smrtsv from the ${SMRT_DIR}, not the python file smrtsv.py. The shell script will setup the environment to find the snakemake install within the dep directory. Since you are running smrtsv.py directly, it's using the Snakemake and Python it finds in your environment, which may create conflicts and may not have all the libraries installed that SMRT-SV uses.

Note: Installing SMRT-SV should not be glitchy. It's pretty well automated now. Pull the git repository, cd into dep, and run make. It shouldn't be dependent on much in your environment; it even uses the conda GCC installation.