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mehdiborji / nanoranger

simplified cellranger for long-read data
MIT License
15 stars 3 forks source link

Error in 5p10XTCR example script #4

Closed EdGreen21 closed 4 months ago

EdGreen21 commented 4 months ago

When running the 5p10XTCR example in a docker container the pipeline runs until the following point and then fails:

...<lines above cut>...
TRA chains: 156 (55.12%)
TRB chains: 127 (44.88%)
TCR_out/TCR_testrun_bcreads.fasta
TCR_out/TCR_testrun_ref/
Feb 19 22:24:35 ..... started STAR run
Feb 19 22:24:35 ... starting to generate Genome files

genomeGenerate.cpp:150:genomeGenerate: exiting because of *OUTPUT FILE* error: could not create output file TCR_out/TCR_testrun_ref//genomeParameters.txt
Solution: check that the path exists and you have write permission for this file

It looks like there might be an error in genomeGenerate.cpp putting in an additional / character into the path for the output file

EdGreen21 commented 4 months ago

pinning the star version to star=2.7.9a fixes this