superstr-screen.py does not complete

[jay-ross]

Hello,

I have successfully run the superSTR software for the processing and postprocessing steps without error, but the motif screening step runs until 19% and then reports an error:

"AttributeError: 'DataFrame' object has no attribute 'append'"

my code looks like this:
superstr-screen.py -m manifest.txt -i input_dir/ -o screen.output.txt --swaplab --min_thresh 1 --controllab control

I am running this on 14 samples, 7 cases and 7 controls, all short-read RNA-sequencing data from fastq. Multiparse and outlier scripts seem to work fine on this data.

Any assistance would be appreciated!

[jay-ross]

The problem turned out to be that installing superSTR through conda has a pandas version more recent than that specified in the installation page (v1.2.2), and in newer pandas versions the append function is deprecated and causes errors. I solved this problem by installing superSTR as follows:

conda install -c bioconda -c conda-forge superstr pandas=1.2.2

[lfearnley]

Great, thanks for the report! I've got a few updates to make to this repo and will add fixing this version requirement in the yml to the list.

…

On Wed, 27 Mar 2024, 4:58 am jay-ross, ***@***.***> wrote: The problem turned out to be that installing superSTR through conda has a pandas version more recent than that specified in the installation page (v1.2.2), and in newer pandas versions the append function is deprecated and causes errors. I solved this problem by installing superSTR as follows: conda install -c bioconda -c conda-forge superstr pandas=1.2.2 — Reply to this email directly, view it on GitHub <#24 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC25LCKUOPBMMQNVAAZN4Q3Y2GZNXAVCNFSM6AAAAABFH6DCYWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRRGEZTCMRUGU> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>