TypeError: list indices must be integers or slices, not NoneType

Danhfg commented 1 year ago

Are you using the latest release? yes

Describe the bug I'm getting the error TypeError: list indices must be integers or slices, not NoneType.

What command did you issue? docker exec 5998245a4a32 funannotate annotate -i */fun/ -o ****/output --cpus 24 --eggnog ***/result.emapper.genepred.gff --busco_db actinopterygii --force Logfiles

[May 24 08:32 PM]: OS: Debian GNU/Linux 10, 24 cores, ~ 132 GB RAM. Python: 3.8.12 [May 24 08:32 PM]: Running 1.8.15 [May 24 08:32 PM]: No NCBI SBT file given, will use default, however if you plan to submit to NCBI, create one and pass it here '--sbt' [May 24 08:32 PM]: Found existing output directory */fun. Warning, will re-use any intermediate files found. [May 24 08:32 PM]: Parsing input files [May 24 08:32 PM]: Existing tbl found: **/*.tbl [May 24 08:39 PM]: Adding Functional Annotation to Brachyplatystoma filamentosum, NCBI accession: None [May 24 08:39 PM]: Annotation consists of: 61,553 gene models [May 24 08:39 PM]: 59,412 protein records loaded [May 24 08:39 PM]: Existing Pfam-A results found: **/annotations.pfam.txt [May 24 08:39 PM]: 28,733 annotations added [May 24 08:39 PM]: Running Diamond blastp search of UniProt DB version 2023_01 [May 24 08:39 PM]: 8,664 valid gene/product annotations from 11,169 total [May 24 08:39 PM]: Existing Eggnog-mapper results found: *****/eggnog.emapper.annotations [May 24 08:39 PM]: Parsing EggNog Annotations [May 24 08:39 PM]: EggNog version parsed as None -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/annotate.py", line 1055, in main EggNog = parseEggNoggMapper(eggnog_result, eggnog_out, GeneProducts) File "/venv/lib/python3.8/site-packages/funannotate/annotate.py", line 338, in parseEggNoggMapper ID = cols[IDi] TypeError: list indices must be integers or slices, not NoneType

OS/Install Information

Checking dependencies for 1.8.15

You are running Python v 3.8.12. Now checking python packages... biopython: 1.81 goatools: 1.2.3 matplotlib: 3.7.1 natsort: 8.3.1 numpy: 1.22.4 pandas: 2.0.0 psutil: 5.9.4 requests: 2.28.2 scikit-learn: 0.24.2 scipy: 1.5.3 seaborn: 0.12.2 All 11 python packages installed

You are running Perl v b'5.026002'. Now checking perl modules... Carp: 1.38 Clone: 0.42 DBD::SQLite: 1.64 DBD::mysql: 4.046 DBI: 1.642 DB_File: 1.855 Data::Dumper: 2.173 File::Basename: 2.85 File::Which: 1.23 Getopt::Long: 2.5 Hash::Merge: 0.300 JSON: 4.02 LWP::UserAgent: 6.39 Logger::Simple: 2.0 POSIX: 1.76 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.12 Tie::File: 1.02 URI::Escape: 3.31 YAML: 1.29 local::lib: 2.000024 threads: 2.15 threads::shared: 1.56 All 27 Perl modules installed

Checking Environmental Variables... $FUNANNOTATE_DB=/opt/databases $PASAHOME=/venv/opt/pasa-2.4.1 $TRINITYHOME=/venv/opt/trinity-2.8.5 $EVM_HOME=/venv/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir

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: 2.4.1 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.3.2 bamtools: bamtools 2.5.2 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.1.6 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: 36.3.8g glimmerhmm: 3.0.4 gmap: 2017-11-15 hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 11.0.8-internal kallisto: 0.46.1 mafft: v7.520 (2023/Mar/22) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: 2.6 proteinortho: 6.0.16 salmon: salmon 0.14.1 samtools: samtools 1.12 snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.9 (July 2021) tantan: tantan 40 tbl2asn: 25.8 tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 ERROR: emapper.py not installed ERROR: gmes_petap.pl not installed ERROR: pslCDnaFilter not installed ERROR: signalp not installed

hyphaltip commented 1 year ago

It looks like eggnog version isn't mapping to what funannotate is expecting. Can you post a snippet of the file you are providing?

Danhfg commented 1 year ago

##gff-version 3
## created with emapper-2.1.10
scaffold1       eggNOG-mapper   CDS     1072    1467    95.1    +       .       ID=scaffold1_80;em_target=7994.ENSAMXP00000014982;em_score=95.1;em_evalue=4.78e-15;em_tcov=15.5;em_searcher=diamond
scaffold1       eggNOG-mapper   CDS     1781    1882    62.4    +       .       ID=scaffold1_81;em_target=7994.ENSAMXP00000014982;em_score=62.4;em_evalue=6.36e-05;em_tcov=5.6;em_searcher=diamond 
.............

nextgenusfs commented 1 year ago

The --eggnog argument is expecting the tab delimited eggnog annotations file not GFF3.

nextgenusfs / funannotate

TypeError: list indices must be integers or slices, not NoneType #917