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Teichlab / tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
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trinity_kmer_length config option not working #102

Open HumzaHemani opened 3 years ago

HumzaHemani commented 3 years ago

Hi,

Setting the trinity_kmer_length option in the config file leads to this error from trinity: ERROR, don't recognize parameter: --KMER_SIZE Based on this, I believe that --KMER_SIZE should be changed to --__KMER_SIZE on line 1093 of tracer_func.py. When running Trinity standalone instead of Tracer, using --__KMER_SIZE instead of --KMER_SIZE works.

Thank you!

mstubb commented 3 years ago

Yes, this has obviously been changed in an update to Trinity. You can either:

  1. Install the last version of Trinity that accepted the old argument

or

  1. Edit the tracer code so that it passes the new argument to the current version of Trinity.

Cheers,

Mike

On 25 Sep 2020, at 21:46, HumzaHemani notifications@github.com wrote:

 Hi,

Setting the trinity_kmer_length option in the config file leads to this error from trinity: ERROR, don't recognize parameter: --KMER_SIZE Based on this, I believe that --KMER_SIZE should be changed to --KMER_SIZE on line 1093 of tracer_func.py. When running Trinity standalone instead of Tracer, using --KMER_SIZE instead of --KMER_SIZE works.

Thank you!

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