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
Please use the formatting bar (especially the
code
option) to present your post better. You can use backticks for inline code (`text` becomestext
), 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.Thanks, much appreciated!