keyerror for sample ID

[Ruonan0101]

Hi,
I try to pass some paired end fastq files in the perseq pipeline and specify the full path in the config file but get the InputFunctionException in line 250 of the Snakefile and the KeyError: <Uniq_sampleID>_multi_multi..not sure why the 'multi' is appended and generate a wired key. Did I miss something and how can I correct this? Thanks~

  File "/home/wuru978/miniconda3/lib/python3.6/site-packages/snakemake/rules.py", line 621, in expand_input
    mapping=mapping)
  File "/home/wuru978/miniconda3/lib/python3.6/site-packages/snakemake/rules.py", line 564, in _apply_wildcards
    item = self.apply_input_function(item, wildcards, **aux_params)
  File "/home/wuru978/miniconda3/lib/python3.6/site-packages/snakemake/rules.py", line 542, in apply_input_function
    raise InputFunctionException(e, rule=self, wildcards=wildcards)
snakemake.exceptions.InputFunctionException: KeyError: 'WD_27_S15_L002_001_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi'
Wildcards:
sample=WD_27_S15_L002_001_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi

InputFunctionException in line 253 of /home/wuru978/Parseq/perseq/Snakefile:
KeyError: 'WD_27_S15_L002_001_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi'
Wildcards:
sample=WD_27_S15_L002_001_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi_multi
unlocking
removed all locks

[colinbrislawn]

Hi @Ruonan0101 ,

I think this looping issue is also described over here :

The advice is to either constrain the wildcard, or, even better, use a prefix for the output that is different from the input.

So maybe L381 and the other rule could be changed so that _multi is a prefix, not a suffix. Maybe this would work:

"gene_catalog/prodigal/multi_{sample}.faa"