snpEff database build error: Error reading codon table- Solved

Question

[wlorenz]

EDIT: Solved. Looks like I somehow accidentally changed the config repository path when modifying snpEff.config: database.repository = http://downloads.sourceforge.net/project/snpeff/databases

I am trying to build a snpEff DB for a bacterial strain that is not represented in the pre-built genomes. Software installation is on a Linux cluster, SnpEff ver. 4.3t 2017-11-24, and I have tried using both a gff3 file and a gtf file (I converted GFF3 w/ gffread utility). I get the same error with both.

First, here is how I edited the config file and specified bacterial codon usage per the manual examples:

data.dir = /scratch/wlorenz/SnpEff_test/data/pantoea971

# P. ananatis, strain 97-1
pantoea971.genome : Pantoea ananatis
pantoea971.chromosomes : NZ_CP020943.1, NZ_CP020944.1, NZ_CP020945.1
pantoea971.NZ_CP020943.1.codonTable : Bacterial_and_Plant_Plastid
pantoea971.NZ_CP020944.1.codonTable : Bacterial_and_Plant_Plastid
pantoea971.NZ_CP020945.1.codonTable : Bacterial_and_Plant_Plastid

And here is my pantoea971 dir. structure where the dir. genomes/ contains the GenBank fasta file renamed pantoea971.fa :

genes.gff
genes.gtf
genomes

The call used is:

java -jar /module/specified/path/snpEff.jar build -c /scratch/wlorenz/SnpEff_test/snpEff.config -gtf22 pantoea971

At first, I was having a problem with the program finding the data files, but I resolved that by adding the full path to the dir. data/ in the config file.

Now, I get this error:

java.lang.RuntimeException: Error reading codon table. Cannot parse entry: '/SCRATCH/WLORENZ/SNPEFF_TEST        : TTT/F'
    Table: '/SCRATCH/QBCG/SNPEFF_TEST       : TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G'
    at org.snpeff.codons.CodonTable.parse(CodonTable.java:285)
    at org.snpeff.codons.CodonTable.<init>(CodonTable.java:71)
    at org.snpeff.snpEffect.Config.createCodonTables(Config.java:148)
    at org.snpeff.snpEffect.Config.readConfig(Config.java:650)
    at org.snpeff.snpEffect.Config.init(Config.java:480)
    at org.snpeff.snpEffect.Config.<init>(Config.java:117)
    at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:364)
    at org.snpeff.SnpEff.run(SnpEff.java:1183)
    at org.snpeff.SnpEff.main(SnpEff.java:162)

If I grep for the selected codon table name in the config file, Bacterial_and_Plant_Plastid, it's there. I also tried to run it without specifying codon usage by commenting out those config lines, but I still get the same error.

Has anyone seen this and/or have a suggestion as to how to mitigate the error?

Thanks,
Walt

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[wlorenz]

Thanks, much appreciated!