Use of uninitialized value $t_g2[1] in hash element at C2_filter_and_select_best_EX_matches_by_targetgene.pl line 70, <INONE> line 2.

[Yuzhang0102]

The log file said "Missing output file(s) PART_*-cluster_input.tab expected by process format_EX_clusters_input".
But in the filter and select best EX matches step, the C2 script report errors nearly in each line...And the filtered_best_scored_EX_matches_by_targetgene.tab is empty. The error is :

Use of uninitialized value $t_g2[1] in hash element at ~/bioapps/ExOrthist-master/bin/C2_filter_and_select_best_EX_matches_by_targetgene.pl line 70, <INONE> line 2.
Use of uninitialized value $t_g2[1] in hash element at ~/bioapps/ExOrthist-master/bin/C2_filter_and_select_best_EX_matches_by_targetgene.pl line 71, <INONE> line 2.
Use of uninitialized value $t_g2[1] in hash element at ~/bioapps/ExOrthist-master/bin/C2_filter_and_select_best_EX_matches_by_targetgene.pl line 72, <INONE> line 2.

Look forward to your reply

[alessiovignoli]

Hello,

do not now if it is still relevant, but I encountered a similar error message:
Use of uninitialized value $l[2] in hash element at ExOrthist/bin/B5_format_aln_info_by_best_isoform_match.pl line 29, <IN> line 2.

It was caused by the fact that my filenames were the following, example:
--genomes Homo-sapiens.fasta --annotations Homo-sapiens.gtf
the --cluster:
GF0001 Homo-sapiens ENSG00001
and --evodists:
Homo-sapiens Mus-musculus short

Basically it seems that the identifier 'Homo-sapiens' (in this case) should be only alphanumerical digits, stuff like '_', '-', ecc. could create troubles and errors. Only tried _ and - :)

hope it can help.