test.groovy

[yelekley]

Hello, I've ran test.groovy bpipe test.groovy to test the pipeline. It looks like it worked, however, it didn't output any bams. Please see the console output below. How to get to run all the scripts to output bams and plots? Thanks

Oct 15 16:21:25 ..... started STAR run
Oct 15 16:21:25 ... starting to generate Genome files
Oct 15 16:21:25 ... starting to sort Suffix Array. This may take a long time...
Oct 15 16:21:25 ... sorting Suffix Array chunks and saving them to disk...
Oct 15 16:21:25 ... loading chunks from disk, packing SA...
Oct 15 16:21:25 ... finished generating suffix array
Oct 15 16:21:25 ... generating Suffix Array index
Oct 15 16:21:25 ... completed Suffix Array index
Oct 15 16:21:25 ... writing Genome to disk ...
Oct 15 16:21:25 ... writing Suffix Array to disk ...
Oct 15 16:21:25 ... writing SAindex to disk
Oct 15 16:21:25 ..... finished successfully
Note: a pattern '%_*.fastq.gz' was provided, but did not match any of the files provided as input [results/genome/Genome].

======================================== Pipeline Succeeded ========================================
16:21:25 MSG:  Finished at Thu Oct 15 16:21:25 EDT 2020
16:21:25 MSG:  Output is results/genome/Genome (pre-existing)