Funannotate-docker compare NOT running

[kalonji08]

Are you using the latest release? If you are not using the latest release of funannotate, please upgrade, if bug persists then report here.

Describe the bug A clear and concise description of what the bug is.

[Nov 18 10:02 PM]: OS: Debian GNU/Linux 10, 40 cores, ~ 99 GB RAM. Python: 3.8.12 [Nov 18 10:02 PM]: Running 1.8.14 [Nov 18 10:02 PM]: Now parsing 1 genomes [Nov 18 10:02 PM]: working on N_albidus_NRRLY1402 [Nov 18 10:02 PM]: No secondary metabolite annotations found [Nov 18 10:02 PM]: Summarizing PFAM domain results [Nov 18 10:02 PM]: Summarizing InterProScan results [Nov 18 10:02 PM]: Loading InterPro descriptions [Nov 18 10:02 PM]: Summarizing MEROPS protease results [Nov 18 10:02 PM]: Summarizing CAZyme results [Nov 18 10:02 PM]: No COG annotations found [Nov 18 10:02 PM]: No SignalP annotations found [Nov 18 10:02 PM]: Summarizing fungal transcription factors [Nov 18 10:02 PM]: No transcription factor IPR domains found Traceback (most recent call last): File "/venv/bin/funannotate", line 8, in sys.exit(main()) File "/venv/lib/python3.8/site-packages/funannotate/funannotate.py", line 716, in main mod.main(arguments) File "/venv/lib/python3.8/site-packages/funannotate/compare.py", line 1067, in main stats[i].append("{0:,}".format(singletons)) TypeError: list indices must be integers or slices, not dict

What command did you issue? funannotate-docker compare -i gbkData/ --cpus 37

Logfiles Please provide relavent log files of the error. funannotate-compare.log

OS/Install Information

• output of funannotate check --show-versions

• version.txt

[nextgenusfs]

Was this genome annotated with funannotate annotate? It doesn't seem to have any of the proper annotations in the genbank file.

[kalonji08]

Hi @nextgenusfs i annotated the genome with funannotate one of our previous colaborator has analysed this genome before and funannotate compare was succesful

[kalonji08]

For funannotate compare the input should be the gbk files right ?

[kalonji08]

Hi @nextgenusfs i hope you are well, i wanted to follow up on the above Error

I run fun annotate predict and annotate on the genomes then copied the gbk files in that folder

Here is the main error: Traceback (most recent call last): File "/home/kalonjilab2/miniconda3/envs/funannotate/bin/funannotate", line 10, in sys.exit(main()) File "/home/kalonjilab2/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 716, in main mod.main(arguments) File "/home/kalonjilab2/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/compare.py", line 1067, in main stats[i].append("{0:,}".format(singletons)) TypeError: list indices must be integers or slices, not str

Its coming from this line

[kalonji08]

Hi @nextgenusfs I run : funannotate test -t compare and it was was succesful. see below

Running funannotate compare unit testing Downloading: https://osf.io/7s9xh/download?version=1 Bytes: CMD: funannotate compare -i Genome_one.gbk Genome_two.gbk Genome_three.gbk -o compare --cpus 40 --ml_model LG+G4 --outgroup botrytis_cinerea.dikarya #########################################################

[Dec 16 07:09 PM]: OS: Ubuntu 20.04, 40 cores, ~ 99 GB RAM. Python: 3.8.13 [Dec 16 07:09 PM]: Running 1.8.13 [Dec 16 07:09 PM]: Now parsing 3 genomes [Dec 16 07:09 PM]: working on Genome one [Dec 16 07:09 PM]: working on Genome two [Dec 16 07:09 PM]: working on Genome three [Dec 16 07:09 PM]: No secondary metabolite annotations found [Dec 16 07:09 PM]: Summarizing PFAM domain results [Dec 16 07:09 PM]: Summarizing InterProScan results [Dec 16 07:09 PM]: Loading InterPro descriptions [Dec 16 07:09 PM]: Summarizing MEROPS protease results [Dec 16 07:09 PM]: found 4 MEROPS familes [Dec 16 07:09 PM]: Summarizing CAZyme results [Dec 16 07:09 PM]: found 5 CAZy familes [Dec 16 07:09 PM]: Summarizing COG results [Dec 16 07:09 PM]: Summarizing secreted protein results [Dec 16 07:09 PM]: Summarizing fungal transcription factors [Dec 16 07:09 PM]: Running GO enrichment for each genome WARNING: skipping Genome_one.txt as no GO terms [Dec 16 07:11 PM]: Running orthologous clustering tool, ProteinOrtho. This may take awhile... [Dec 16 07:11 PM]: Compiling all annotations for each genome [Dec 16 07:11 PM]: Inferring phylogeny using iqtree [Dec 16 07:11 PM]: Found 1 single copy BUSCO orthologs, will use all to infer phylogeny [Dec 16 07:13 PM]: Compressing results to output file: compare.tar.gz [Dec 16 07:13 PM]: Funannotate compare completed successfully! ######################################################### SUCCESS: funannotate compare test complete. #########################################################