snippy_multi fails to load reads

[shawndy]

Running one sample at a time works OK, can't create runme.sh

$snippy-multi input.tab --report --html --cpus 7 --ref /home/shawndy/Biomatics/snippy/C01_assembly.fasta > runme.sh

causes: ERROR: [C01_/home/shawndy/Biomatics/snippy/C01/Sample1.R1.fastq_/home/shawndy/Biomatics/snippy/C01/Sample1.R2.fastq] missing read/contig data: C01 /home/shawndy/Biomatics/snippy/C01/Sample1.R1.fastq /home/shawndy/Biomatics/snippy/C01/Sample1.R2.fastq

input.tab =

input.tab = ID R1 [R2]

C01 /home/shawndy/Biomatics/snippy/C01/Sample1.R1.fastq /home/shawndy/Biomatics/snippy/C01/Sample1.R2.fastq C02 /home/shawndy/Biomatics/snippy/C02/Sample2.R1.fastq /home/shawndy/Biomatics/snippy/C02/Sample2.R2.fastq

(etc. for seven samples, no hard return at end, crated in text editor, all separators are tabs)

I tried with the .gz compressed versions as well, same error. Mint linux. Snippy 4.6.0.

[shawndy]

oops, the formatter made the variable input tab huge text, sorry.

[andersgs]

Hi @shawndy. The errors seems to imply that either the path is wrong, or the formatting is incorrect.

Can you confirm the path is correct with:

ls /home/shawndy/Biomatics/snippy/C01/Sample1.R1.fastq

And, can you confirm that the tabs haven't accidentally been transformed to spaces with:

od -c input.tab

You should see \t between the filed in a line, and \n between lines for that last command.

Anders.

[vissli]

Found this after encountering the same problem. od -c input.tab revealed a trailing tab at the end of my input file and removing this solved the issue for me.