Problem: My InterProScan with nucleotide fastas as input among which there are multiple fastas with non-unique names consistently returns no output
Description: I'm running InterProScan (InterProScan-5.21-60.0) search on linux in standalone mode. In test searches, when I'm looking only for GO terms and search Pfam database and I use the test multifasta provided in InterProScan package (test_nt_redundant.fasta) which includes also some fastas different in sequence but with non-unique names (see below), the analysis runs without any problems.
interproscan.sh -i test_nt_redundant.fasta -b output -goterms -appl Pfam -t n
The fasta headers in the test file are:
>A2YIW7 >Bob >ENA|AACH01000026|AACH01000026.1 Saccharomyces mikatae IFO 1815 YM4906-Contig2858, whole genome shotgun sequence. >ENA|AACH01000027|AACH01000027.2 Saccharomyces mikatae IFO 1815 YM4906-Contig2858, whole genome shotgun sequence. >Henry >reverse translation of P22298 >reverse translation of P22298 >Wilf
However, when I run the same analysis with a set of 15 fastas which I'd like to annotate and which contains also some fastas with non-unique identifiers, I'm consistently receiving following massage and interproscan ends without any output:
Found 3 non unique identifier(s). These identifiers do have different sequences, within the FASTA nucleotide sequence input file. Please find below a list of detected identifiers: 100646091 100646573 100645787 InterProScan will shutdown, because there is no way to map nucleic sequences and predicted proteins.
Remarkably, even the returned list of non-unique identifiers is not complete. (see below for the list of fasta headers in the 15fasta set):
>100645110 >100645230 >100645431 >100645550 >100645666 >100645666 >100645666 >100645787 >100645787 >100645973 >100646091 >100646091 >100646214 >100646573 >100646573
Additionaly, when I remove from the 15fasta set the non-unique fastas, the analysis runs without any problem - so I guess the problem is somehow connected to the number of non-unique fasta identifiers in the input.
I'm wondering what might be the source of this error and how to solve it? Thanks in advance for any hints.