ERROR: exonerate

[alexvasilikop]

Hello I am using version 1.8.11

I ran the funnanotate command as follows: $ funannotate predict -i $genome -o $outdir_predict -s "species" --cpus 10 \
--protein_evidence $uniprot $uniref50 --rna_bam $rna_bam --busco_db metazoa
--organism other --ploidy 1 --repeats2evm

Now the pipeline does not break (still running at exonerate step) but an error pops up (see below) I get as output:

---

[Aug 08 11:00 AM]: OS: Ubuntu 18.10, 48 cores, ~ 264 GB RAM. Python: 3.8.12 [Aug 08 11:00 AM]: Running funannotate v1.8.11 [Aug 08 11:00 AM]: Skipping CodingQuarry as --organism=other. Pass a weight larger than 0 to run CQ, ie --weights codingquarry:1 [Aug 08 11:00 AM]: Parsed training data, run ab-initio gene predictors as follows: Program Training-Method augustus busco
genemark selftraining
glimmerhmm busco
snap busco
[Aug 08 11:01 AM]: Loading genome assembly and parsing soft-masked repetitive sequences [Aug 08 11:01 AM]: Genome loaded: 6 scaffolds; 111,436,876 bp; 4.96% repeats masked [Aug 08 11:01 AM]: Extracting hints from RNA-seq BAM file using bam2hints [Aug 08 11:11 AM]: Mapping 51,380,413 proteins to genome using diamond and exonerate [Aug 08 06:18 PM]: Found 7,006,091 preliminary alignments with diamond in 3:56:56 --> generated FASTA files for exonerate in 3:09:30 ERROR: exonerate --model p2g --showvulgar no --showalignment no --showquerygff no --showtargetgff yes --maxintron 3000 --percent 80 --ryo AveragePercentIdentity: %pi /tmp/p2g_4218a539-c6d1-4c39-b955-86fdb9f09405/proteins/UniRef50_A0A126QW58.fasta /tmp/p2g_4218a539-c6d1-4c39-b955-86fdb9f09405/scaffolds/contig_4_1326970-1348678.fasta ERROR: exonerate --model p2g --showvulgar no --showalignment no --showquerygff no --showtargetgff yes --maxintron 3000 --percent 80 --ryo AveragePercentIdentity: %pi /tmp/p2g_4218a539-c6d1-4c39-b955-86fdb9f09405/proteins/UniRef50_A0A126QW58.fasta /tmp/p2g_4218a539-c6d1-4c39-b955-86fdb9f09405/scaffolds/contig_5_2962019-2983660.fasta ERROR: exonerate --model p2g --showvulgar no --showalignment no --showquerygff no --showtargetgff yes --maxintron 3000 --percent 80 --ryo AveragePercentIdentity: %pi /tmp/p2g_4218a539-c6d1-4c39-b955-86fdb9f09405/proteins/UniRef50_A0A126QW58.fasta /tmp/p2g_4218a539-c6d1-4c39-b955-86fdb9f09405/scaffolds/contig_6_9394155-9416045.fasta Progress: 13.67%

What might be the issue? Thanks

[gchevignon]

Hello, I just got the same error ... Did you find any solution to fix it ? Best