funannotate: eggnog v2 output is not being parsed correctly
Am getting the following error when running annotate on my isolates. The same problem occurs even when providing pre-processed results using --antismash and --eggnog flags.
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[05:15 PM]: OS: Ubuntu 20.04, 12 cores, ~ 33 GB RAM. Python: 3.8.5
[05:15 PM]: Running 1.8.4
[05:15 PM]: Found existing output directory funannotate_output/isolate1. Warning, will re-use any intermediate files found.
[05:15 PM]: Parsing input files
[05:15 PM]: Existing tbl found: funannotate_output/isolate1/predict_results/isolate1.tbl
[05:15 PM]: Adding Functional Annotation to Ascochyta rabiei, NCBI accession: None
[05:15 PM]: Annotation consists of: 10,616 gene models
[05:15 PM]: 10,364 protein records loaded
[05:15 PM]: Existing Pfam-A results found: funannotate_output/isolate1/annotate_misc/annotations.pfam.txt
[05:15 PM]: 11,652 annotations added
[05:15 PM]: Running Diamond blastp search of UniProt DB version 2021_01
[05:15 PM]: 725 valid gene/product annotations from 1,061 total
[05:15 PM]: Existing Eggnog-mapper results found: funannotate_output/isolate1/annotate_misc/eggnog.emapper.annotations
[05:15 PM]: Parsing EggNog Annotations
[05:15 PM]: 0 COG and EggNog annotations added
[05:15 PM]: Combining UniProt/EggNog gene and product names using Gene2Product version 1.65
[05:15 PM]: 725 gene name and product description annotations added
[05:15 PM]: Existing MEROPS results found: funannotate_output/isolate1/annotate_misc/annotations.merops.txt
[05:15 PM]: 361 annotations added
[05:15 PM]: Existing CAZYme results found: funannotate_output/isolate1/annotate_misc/annotations.dbCAN.txt
[05:15 PM]: 511 annotations added
[05:15 PM]: Existing BUSCO2 results found: funannotate_output/isolate1/annotate_misc/annotations.busco.txt
[05:15 PM]: 1,279 annotations added
[05:15 PM]: Skipping phobius predictions, try funannotate remote -m phobius
[05:15 PM]: Existing SignalP results found: funannotate_output/isolate1/annotate_misc/signalp.results.txt
[05:15 PM]: 1,060 secretome and 0 transmembane annotations added
[05:15 PM]: Parsing InterProScan5 XML file
[05:15 PM]: Now parsing antiSMASH v6 results, finding SM clusters
[05:15 PM]: Found 0 clusters, 0 biosynthetic enyzmes, and 0 smCOGs predicted by antiSMASH
[05:15 PM]: Found 0 duplicated annotations, adding 44,471 valid annotations
[05:15 PM]: Converting to final Genbank format, good luck!
[05:16 PM]: Creating AGP file and corresponding contigs file
[05:16 PM]: Cross referencing SM cluster hits with MIBiG database version 1.4
[05:16 PM]: CMD ERROR: diamond blastp --sensitive --query funannotate_output/isolate1/annotate_misc/antismash/smcluster.proteins.fasta --threads 12 --out funannotate_output/isolate1/annotate_misc/antismash/smcluster.MIBiG.blast.txt --db /home/fredrick/funannotate_db/mibig.dmnd --max-hsps 1 --evalue 0.001 --max-target-seqs 1 --outfmt 6
b'diamond v0.9.26.127 | by Benjamin Buchfink <buchfink@gmail.com>\nLicensed under the GNU GPL <https://www.gnu.org/licenses/gpl.txt>\nCheck http://github.com/bbuchfink/diamond for updates.\n\n#CPU threads: 12\nScoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)\nTemporary directory: funannotate_output/isolate1/annotate_misc/antismash\nOpening the database... [0.000575s]\n#Target sequences to report alignments for: 1\nOpening the input file... [5.7e-05s]\nError: Error detecting input file format. First line seems to be blank.\n'```About this issue
- Original URL
- State: closed
- Created 3 years ago
- Comments: 30 (22 by maintainers)
Commits related to this issue
- update eggnog parser for v2 release and added EC_numbers from eggnog #566 — committed to nextgenusfs/funannotate by deleted user 3 years ago
- parser for eggnog v2.1.2 and greater #566 — committed to nextgenusfs/funannotate by deleted user 3 years ago
Perhaps it’s on pip?
Okay, well that’s not great for several reasons, but it actually got at least the v2 parser… problem is that hash is going to always evaluate as greater than… even if it was a hash from a version that is not there. But the problem here is the altered headers again. So I’ll try to fix it for this one… but I’ll open an issue – I do not have the time to update this every few weeks.
Okay, well this
max_annot_lvlis definitely a new header. Really sucks this keeps changing… not sure I have the patience to constantly update this…Hi there, I just run
funannotate annotate(v1.8.7) with EggNOG mapper results generated externally (emapper.py v2.1.2) and funannotate fails to parse every single annotation. Apparently some changes have been made to the output files of emapper in the last release (https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.2#v212)Thanks @nextgenusfs . Everything works okay now.
Here is the progress from a few of the isolates I was analysing
With this update
funannotate comparealso runs well without any hiccups.