test errors

[zhangwenda0518]

I need your help ！ when i run it errors happened

funannotate util prot2genome -g test.softmasked.fa -p protein.evidence.fasta -o test

[Mar 13 02:12 PM]: Mapping 1,065 proteins to genome using diamond and exonerate [Mar 13 02:12 PM]: Found 1,505 preliminary alignments with diamond in 0:00:04 --> generated FASTA files for exonerate in 0:00:00 Traceback (most recent call last): File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/funannotate/aux_scripts/funannotate-p2g.py", line 349, in progress=args.progress) File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/funannotate/library.py", line 1266, in runMultiProgress if x.successful(): File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/multiprocessing/pool.py", line 631, in successful assert self.ready() AssertionError

########################################################################################### version ：

Checking dependencies for 1.8.14

You are running Python v 3.6.15. Now checking python packages... biopython: 1.79 goatools: 1.2.3 matplotlib: 3.3.4 natsort: 8.2.0 numpy: 1.19.5 pandas: 1.1.5 psutil: 5.8.0 requests: 2.28.1 scikit-learn: 0.24.2 scipy: 1.1.0 seaborn: 0.11.2 All 11 python packages installed

You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.38 Clone: 0.46 DBD::SQLite: 1.72 DBD::mysql: 4.050 DBI: 1.643 DB_File: 1.855 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 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: 2.000029 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed

Checking Environmental Variables... $FUNANNOTATE_DB=/home/zhangwenda/database/funannotate_db $PASAHOME=/home/zhangwenda/sysoft/anaconda3/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/home/zhangwenda/sysoft/anaconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/home/zhangwenda/sysoft/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/home/zhangwenda/sysoft/anaconda3/envs/funannotate/config/ $GENEMARK_PATH=/home/zhangwenda/biosoft/gene_prediction/gmes_linux_64_4 All 6 environmental variables are set

Checking external dependencies... 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: 2.1.4 emapper.py: v1.0 ete3: 3.1.1 exonerate: exonerate 2.2.0 fasta: 36.3.8g glimmerhmm: 3.0.4 gmap: 2017-11-15 gmes_petap.pl: 4.69_lic hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 11.0.1 kallisto: 0.46.1 mafft: v7.515 (2023/Jan/15) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: 2.4 proteinortho: 6.2.0 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.16.1 signalp: 5.0b 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 All 37 external dependencies are installed

[zhangwenda0518]

I've been stuck here for a long time. Could you please give me some help?

[nextgenusfs]

I can't tell from your output what the error is, I'd try to downgrade diamond. See here https://github.com/nextgenusfs/funannotate/issues/872

[zhangwenda0518]

I tried his last answer many times, but I still didn't succeed

I tried tblastn instead of diamond, but this error occurred.

/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/funannotate-1.8.14-py3.6.egg/funannotate/aux_scripts/funannotate-p2g.py -p annotate/predict_misc/proteins.combined.fa -g /home/zhangwenda/soft-test/funannotate/test-predict_c93fd7c6-4369-4af6-af0f-2d3070b3d749/annotate/predict_misc/genome.softmasked.fa --maxintron 3000 --exonerate_pident 80 --ploidy 1 **-f tblastn** --tmpdir ./tmp --tblastn_out annotate/predict_misc/p2g.diamond.out -o test

errors

[Mar 21 11:22 PM]: Mapping 1,065 proteins to genome using tblastn and exonerate
Traceback (most recent call last):
  File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/funannotate-1.8.14-py3.6.egg/funannotate/aux_scripts/funannotate-p2g.py", line 322, in <module>
    outfile.write('>{}\n{}\n'.format(x[0], lib.softwrap(str(genome_dict[x[0]].seq))))
  File "/home/zhangwenda/sysoft/anaconda3/envs/funannotate/lib/python3.6/site-packages/Bio/File.py", line 248, in __getitem__
    record = self._proxy.get(self._offsets[key])
KeyError: 'gb|CP022974.1|'

this file

how I can do ？ I've been troubled for nearly two weeks. I once ran it successfully on another server.

[nextgenusfs]

If you can run the tests and they pass then it's your input data. If tests don't pass then it's your install.... sounds like from recent other post that newest version of diamond is fixed. As per this error I'm not sure other than your fasta headers are certainly not ideal, I would get rid of those pipes in the headers.

[zhangwenda0518]

I downgraded diamond to 2.0.8, but the error remains.

[zhangwenda0518]

The good news is that I solved this mistake.

The error message stayed in the very early stage of prediction. I tried to manually install different versions of augustus and diamond myself. tblastn still had errors in the test data. Similarly, I tried to add my transcription group data to my personal data set, and let him use tinity to assemble it again, and the errors still occurred.These eliminate the problem of software installation. So I checked my python environment. In order to solve the conda installation problem of ete3, I specified ### python=3.6 when I created the environment. Considering that I don't need ete3, I decided to sacrifice ete3 and upgrade python to version 3.8.15. it also successfully run on test data.

I re-created a new environment, using only the following commands. mamba create -n funannotate funannotate

I can run on my sequencing data normally. One disadvantage is that ete3 is still wrong at this time, but other functions of funannotate are enough to meet my needs.

the errors of ete3 is

Have you ever encountered this mistake? And how can I solve it?

[nextgenusfs]

Yeah that is a common error with that package. I don't recall the fox, but ete3 would only be used for funannotate compare so the rest of the tools should work without it.