"Line 7 did not have 2 elements" Error

[jack-d-barber]

Hi Fiona,

I'm getting error messages after trying to run Coinfinder on two different datasets (both of which are small "test" datasets I'm happy to share if required).

ERROR MESSAGE FROM R: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 7 did not have 2 elements Calls: read.table -> scan Execution halted

It looks like the program only gets so far before this error which appears at the same point for both coincident (error msg above) and avoidant analyses. I've included the head of the _edges and _nodes coincident .tsv files below.

(base) r03jb21@MD-058326:/mnt/c/Users/r03jb21/Documents/2023-04_aopp_course/2023-06-29_100ecoli_trial/d_coinfinder/from_roary$ head coincident_results_edges.tsv
Source  Target  weight
COQ3    group_2156      0.000852968
COQ3    speF_2  0.000852968
COQ3    group_253       0.000852968
COQ3    group_2564      0.014703
COQ3    group_2601      0.000852968
COQ3    group_47        0.014703
COQ3    group_5355      0.014703
COQ3    group_5561      0.000852968
COQ3    group_5642      0.014703

(base) r03jb21@MD-058326:/mnt/c/Users/r03jb21/Documents/2023-04_aopp_course/2023-06-29_100ecoli_trial/d_coinfinder/from_roary$ head coincident_results_nodes.tsv
ID      Result
group_2907      0.319012923670881
yajI    -1.26396258750936
group_20154     1.12897208596648
group_2920      0.529872856421225
group_2929      0.214793780969454
rimI    1.11956292692888
group_294       0.386142612892017holD   1.11027705462035

yhcH_1  -1.3138334182027

Many thanks for your help!

Cheers, Jack

[fwhelan]

Hi Jack,

Sorry you're having issues with coinfinder. Could you confirm that your _nodes.tsv file is showing the data for group_294 and holD on the same line (and not just a quirk of github's formatting)?

Thanks.

[jack-d-barber]

Hi Fiona,

Yes holD and group_294 are on the same line in the .tsv file. I had a quick look at the avoidance_result_nodes.tsv file and the same thing appears in two places there.

Cheers!

[fwhelan]

Hi Jack, that's strange, I haven't seen that before! Would you be willing to share your inputs for me to test locally?