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Kingsford-Group / ribomap

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Pipeline failing a riboprof #12

Open hector3500 opened 9 months ago

hector3500 commented 9 months ago

Hi, I am using the pipeline for riboseq analysis and other than a couple of slight changes (just some salmon commands), it is working fine until the riboprof section, where this error is being displayed:

getting transcript info... total number of transcripts in transcriptome: 34544 assigning ribo-seq reads... constructing profile class... terminate called after throwing an instance of 'std::invalid_argument' what(): stod ./run_ribomap.sh: line 325: 13994 Aborted (core dumped) riboprof ${options} pipeline failed at ribosome profile generation!

Do you have any idea what the issue could be? Thanks, Harrison

how-wonderful commented 9 months ago

Hi @hector3500 Thank you for your interest in using Ribomap. While it's delighted to see that ribomap is still being tested after seven years since its release, the tool itself is not actively maintained, and it only supports specific dependency versions. For troubleshooting, please make sure to use the correct versions of the prerequisites. For example, if you are compiling the executable from source, please use seqan version 1.4.1 (http://packages.seqan.de/).

You could also check whether the intermediate files have the same format as the test case. If different versions of dependencies generate different file formats, you might need to revise those files to match the format.

Good luck!