egluckthaler / starfish Goto Github PK

I believe that the annotate command in the step-by-step tutorial has a typo:

starfish annotate -T 2 -x macpha6_tyr -a ome2assembly.txt -g macpha6.gff3 -p ../database/YRsuperfams.p1-512.hmm -P ../database/YRsuperfamRefs.faa -i tyr -o geneFinder/

Where the -g parameter should be ome2gff.txt instead of macpha6.gff3.

Thanks for the fantastic programme!

From: https://github.com/egluckthaler/starfish/wiki/Installation

when replacing the cnef.cc file, your instructions say:
cp ../scripts/cneff.cc .

but it should say:
cp ../scripts/cnef.cc .

I guess this is a bit of a dangerous error, and might pop up due to other install errors. Since the original file and the new file have the same names, it is hard to distinguish between them.

I guess an option would be to rename your cnef.cc to cnef_starfish.cc

and then add a sed command for the Makefile? Something like this?
sed -i "s/cnef.cc/cnef_starfish.cc/" Makefile

Hello Emile and group! Excited to try your program on my Histoplasma datasets but I have hit a couple of snags, some I've solved but currently stuck on this one.

I have been following your tutorial for your test dataset and the portion I have been stuck on is your eggnog annotation sorting.
My genomes have been annotated using Funannotate, but I also attempted an eggnog-mapper run and my output does not look like yours.

Your step that cuts your emapper into a text file for later steps is giving me an issue:

cut -f1,10 ann/*emapper.annotations | grep -v '#' | perl -pe 's/^([^\s]+?)\t([^\|]+).+$/\1\t\2/' > ann/macph6.gene2og.txt

the -f1,10 cut is looking for "bestOG|evalue|score" tab where it pulls out the first portion "bestOG" to create the text file. Is it maybe a -flag I am missing for this specific emapper output?

Funannotate:
GeneID TranscriptID Feature Contig Start Stop Strand Name Product Alias/Synonyms EC_number BUSCO PFAM InterPro EggNog COG GO Terms Secreted Membrane Protease CAZyme Notes gDNA mRNA CDS-transcript Translation
19VMG-15_000001 19VMG-15_000001-T1 mRNA scaffold_1 63793 65897 + hypothetical protein 2.1.1.310 EOG091P0ENB PF01189;PF17125 IPR001678 SAM-dependent methyltransferase RsmB-F/NOP2-type domain;IPR011023 Nop2p;IPR018314 Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site;IPR023267 RNA (C5-cytosine) methyltransferase;IPR023273 RNA (C5-cytosine) methyltransferase, NOP2;IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily;IPR031341 Ribosomal RNA small subunit methyltransferase F, N-terminal ENOG503NUZ7 L:(L) Replication, recombination and repair GO_component: GO:0005730 - nucleolus [Evidence IEA];GO_function: GO:0008757 - S-adenosylmethionine-dependent methyltransferase activity [Evidence IEA];GO_function: GO:0008168 - methyltransferase activity [Evidence IEA];GO_function: GO:0003723 - RNA binding [Evidence IEA];GO_function: GO:0009383 - rRNA (cytosine-C5-)-methyltransferase activity [Evidence IEA];GO_process: GO:0006396 - RNA processing [Evidence IEA];GO_process: GO:0001510 - RNA methylation [Evidence IEA];GO_process: GO:0070475 - rRNA base methylation [Evidence IEA];GO_process: GO:0000470 - maturation of LSU-rRNA [Evidence IEA]

My eggnog-mapper:
#query seed_ortholog evalue score eggNOG_OGs max_annot_lvl COG_category Description Preferred_name GOs EC KEGG_ko KEGG_PathwayKEGG_Module KEGG_Reaction KEGG_rclass BRITE KEGG_TC CAZy BiGG_Reaction PFAMs
01_16_1 5037.XP_001538943.1 0 3312 COG1020@1|root,KOG1178@2759|Eukaryota,38V1T@33154|Opisthokonta,3Q08R@4751|Fungi,3R2AF@4890|Ascomycota,20DTP@147545|Eurotiomycetes,3AZS6@33183|Onygenales 4751|Fungi Q Condensation domain - - - ko:K22152 - - - ko00000 - - - AMP-binding,Condensation,PP-binding

Your eggnog-mapper:
#query_name seed_eggNOG_ortholog seed_ortholog_evalue seed_ortholog_score predicted_gene_name GO_terms KEGG_pathways Annotation_tax_scope OGs bestOG|evalue|score COG cat eggNOG annot
mp040_13792 441959.XP_002479979.1 5.00E-71 232.2 FG02084.1 GO:0005575,GO:0005623,GO:0005886,GO:0006810,GO:0008150,GO:0015886,GO:0016020,GO:0016021,GO:0031224,GO:0044425,GO:0044464,GO:0044699,GO:0044765,GO:0051179,GO:0051181,GO:0051234,GO:0071702,GO:0071705,GO:0071944,GO:1901678 fuNOG[21] 03RFZ@ascNOG,0IWNB@euNOG,0M5FN@euroNOG,0MQ5B@eurotNOG,0PN5J@fuNOG,11Q0B@NOG,13QP8@opiNOG 0PN5J|7.70053432588e-86|288.860290527 S RTA1 domain protein

Any guidance would be appreciated!

-Tania

hey i do now what is wrong...

(starfish) marcin@marcin-:~/starfish/test$ starfish annotate -T 2 -x macpha6_tyr -a ome2assembly.txt -g ome2gff.txt -p ../db/YRsuperfams.p1-512.hmm -P ../db/YRsuperfamRefs.faa -i tyr -o geneFinder/
[Thu Apr 25 21:33:47 2024] executing command: starfish annotate -T 2 -x macpha6_tyr -a ome2assembly.txt -g ome2gff.txt -p ../db/YRsuperfams.p1-512.hmm -P ../db/YRsuperfamRefs.faa -i tyr -o geneFinder/
Key parameters:
metaeuk        -v 3 -s 7.5 -e 0.0001 --max-intron 2000 --max-seqs 300 --metaeuk-eval 0.001 --exhaustive-search 1 --metaeuk-tcov 0.25 --allow-deletion 1 --protein 1 --disk-space-limit 100G --compressed 1
hmmsearch      --max -E 0.001

[Thu Apr 25 21:33:47 2024] geneFinder//macpha6_tyr.fas exists, skipping metaeuk annotation
[Thu Apr 25 21:33:47 2024] geneFinder//macpha6_tyr.hmmout exists, skipping HMM annotation of metaeuk results
[Thu Apr 25 21:33:47 2024] filtering metaeuk annotations based on hmmsearch results..
[Thu Apr 25 21:33:47 2024] lifting over names of overlapping feature from GFFs in ome2gff.txt to metaeuk annotations..
[Thu Apr 25 21:33:47 2024] checking formatting of GFFs in ome2gff.txt..
sh: 1: Syntax error: "(" unexpected

cheers