returned non-zero exit status 1 in funannotate update

[hassantarabai]

Hello,

I am having a new error when running funannotate update, The workflow seems to run normally but generate an error when reaching the final step in converting to genebank format and collecting annotation files.

Here is the generated error "

Traceback (most recent call last): File "/home/miniconda3/envs/funannotate/bin/funannotate", line 8, in sys.exit(main()) File "/home/miniconda3/envs/funannotate/lib/python3.7/site-packages/funannotate/funannotate.py", line 716, in main mod.main(arguments) File "/home/miniconda3/envs/funannotate/lib/python3.7/site-packages/funannotate/update.py", line 2485, in main transcripts=allGFF3, previous=existingStats) File "/home/miniconda3/envs/funannotate/lib/python3.7/site-packages/funannotate/library.py", line 2622, in annotation_summary for line in execute(cmd): File "/home/miniconda3/envs/funannotate/lib/python3.7/site-packages/funannotate/library.py", line 555, in execute raise subprocess.CalledProcessError(return_code, cmd) subprocess.CalledProcessError: Command '['bedtools', 'intersect', '-a', 'tmp.exon.4182799.bed', '-u', '-f', '0.9', '-s', '-b', '../prediction01/update_misc/transcript.alignments.gff3']' returned non-zero exit status 1."

Anybody faced this error ?

The error suggests a problem with bedtools (i have version 2.30 installed).. i will try to downgrade it and see if it will make any difference.

Here is the output from funannotate check --show-versions You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.50 Clone: 0.46 DBD::SQLite: 1.72 DBD::mysql: 4.046 DBI: 1.643 DB_File: 1.855 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.27 Getopt::Long: 2.54 Hash::Merge: 0.302 JSON: 4.10 LWP::UserAgent: 6.67 Logger::Simple: 2.0 POSIX: 1.94 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.14 Tie::File: 1.06 URI::Escape: 5.12 YAML: 1.30 local::lib: 2.000028 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed

$FUNANNOTATE_DB=/home/funannotate_db $PASAHOME=/home/miniconda3/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/home/miniconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/home/miniconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/home/miniconda3/envs/funannotate/config/ $GENEMARK_PATH=/home/gene_mark/gmes_linux_64_4/ All 6 environmental variables are set

Checking external dependencies... ERROR: pslDnaFiler found but error running: pslCDnaFilter: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory

PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.5.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.1.6 emapper.py: 2.1.10 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: 36.3.8g glimmerhmm: 3.0.4 gmap: 2021-08-25 hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 17.0.3-internal kallisto: 0.46.1 mafft: v7.520 (2023/Mar/22) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: 2.4 proteinortho: 6.2.2 salmon: salmon 0.14.1 samtools: samtools 1.16.1 signalp: 6.0 snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.11 (Oct 2022) tantan: tantan 40 tbl2asn: 25.8 tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 ERROR: gmes_petap.pl not installed ERROR: pslCDnaFilter not installed

[hyphaltip]

have you run bedtools intersect on its own?

[hassantarabai]

@hyphaltip

Bedtools intersect indicate "scaffold_11 15750302 15750296 FUN_021423-T1.exon1 . -" as the error.

Removing it from the file solve the error but am not sure how the error was generated.