I tried deploying, and ran into:
[MMAdeploy] DEBUG 12:36:05: Examining ftp.sra.ebi.ac.uk for test dataset
[MMAdeploy] ERROR 12:36:20: ftp connection to ftp.sra.ebi.ac.uk could not be established. Are you firewalled?
Check whether ftp ports are openned (default is often 20, 21 or 990). Skipping host!
[...]
[MMAseq] WARNING 12:36:20: Unable to resolve sample path: reads/ERR3528110_1.fastq.gz. Skipping!
[MMAseq] WARNING 12:36:20: Unable to resolve sample path: reads/ERR3528110_2.fastq.gz. Skipping!
[...]
[MMAseq Pipeline] INFO 12:36:24: Building DAG of jobs...
MissingInputException in rule custom_kmeralignment in file "/Users/b507595/code/mmaseq/src/mmaseq/workflow/rules/mappers.smk", line 1:
Missing input files for rule custom_kmeralignment:
output: /Users/b507595/Downloads/mmaseq/deploy/MMAseq_Test/ERR3528110/raw/kmeraligner/ecoligenes.res, /Users/b507595/Downloads/mmaseq/deploy/MMAseq_Test/ERR3528110/raw/samtools/ecoligenes.sam, /Users/b507595/Downloads/mmaseq/deploy/MMAseq_Test/ERR3528110/raw/kmeraligner/ecoligenes.mat.gz
wildcards: sample=ERR3528110, database=ecoligenes
affected files:
reads/ERR3528110_1.fastq.gz
reads/ERR3528110_2.fastq.gz
Maybe my fault for running with high verbosity, meaning I missed these clues initially. However, I think that code that logs an error should probably also throw an exception.
I tried deploying, and ran into:
Maybe my fault for running with high verbosity, meaning I missed these clues initially. However, I think that code that logs an error should probably also throw an exception.