Comments (2)
I found the problem:
When you specify a TSV file, e.g. hecatomb run --reads samples.tsv, Hecatomb expects a 3-column tab separated file with the first column specifying the sample name, and the other columns the relative or full paths to the forward and reverse read files. e.g.
sample1 /path/to/reads/sample1.1.fastq.gz /path/to/reads/sample1.2.fastq.gz
sample2 /path/to/reads/sample2.1.fastq.gz /path/to/reads/sample2.2.fastq.gz
I inadvertently had a space in the sample name
sample 1
Might be worth adding to docs, "If you specify a TSV file and Hecatomb fails immediately, check your TSV file for spaces"
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Actually, I should add a check for spaces in file names when reading from a TSV.
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