MLST scheme for ecloacae not found

[hkunerth]

Description of the bug

Hi,

I'm doing some testing of the Phoenix pipeline and ran a set of E cloacae through, but the pipeline failed on the MLST step with the following error:

[18:48:21] This is mlst 2.25.0 running on linux with Perl 5.038002
[18:48:21] Checking mlst dependencies:
[18:48:21] Found 'blastn' => /usr/bin/blastn
[18:48:21] Found 'any2fasta' => /usr/local/bin/any2fasta
[18:48:21] Found blastn: 2.12.0+ (002012)
[18:48:21] Invalid --scheme 'ecloacae'. Check using --list

I ran the container (quay.io-jvhagey-mlst@sha256-a67904d356118f9c163d26000d4d78cc449e3205145f87be28726869d67602f7.img) in Apptainer and listed the schemes that are available:

aactinomycetemcomitans
abaumannii
abaumannii_2
achromobacter
actinobacillus
aeromonas
afumigatus
aparagallinarum_Ghanem
aparagallinarum_Guo
aphagocytophilum
arcobacter
bbacilliformis
bcc
bcereus
bfragilis
bhampsonii
bhenselae
bhyodysenteriae
bintermedia
blastocystis
blicheniformis
bordetella
borrelia
bpilosicoli
bpseudomallei
brachyspira
brucella
bsubtilis
btrachomatis
btrachomatis-uppsala
bwashoensis
cacnes
calbicans
cbotulinum
cconcisus
cdifficile
cdiphtheriae
cfetus
cglabrata
chelveticus
chlamydiales
chyointestinalis
cinsulaenigrae
citrobacter
cjejuni
ckrusei
clanienae
clari
cliberibacter
cmaltaromaticum
cperfringens
cronobacter
csepticum
csinensis
csputorum
ctropicalis
cupsaliensis
dnodosus
ecoli
ecoli_2
edwardsiella
efaecalis
efaecium
efaecium_Bezdicek
enterobacter
fpsychrophilum
ganatis
geotrichum
gparasuis
hcinaedi
hinfluenzae
hpylori
hsuis
kaerogenes
kkingae
klebsiella
koxytoca
kseptempunctata
leptospira
leptospira_2
leptospira_3
lgarvieae
lmonocytogenes
lsalivarius
mabscessus
magalactiae
manserisalpingitidis
mbovis
mbovis_legacy
mcanis
mcaseolyticus
mcatarrhalis
mflocculare
mgallisepticum_Beko
mgallisepticum_Ghanem
mgenitalium
mhaemolytica
mhominis
mhyopneumoniae
mhyorhinis
mhyosynoviae
miowae
mmorganii
mplutonius
mpneumoniae
msciuri
msynoviae
mycobacteria
neisseria
orhinotracheale
otsutsugamushi
paeruginosa
pdamselae
pfluorescens
pgingivalis
plarvae
pmultocida_multihost
pmultocida_rirdc
ppentosaceus
pputida
proteus
providencia
psalmonis
pstuartii
ranatipestifer
rhodococcus
sagalactiae
salmonella_Achtman
salmonella_Oxford
saureus
sbsec
scanis
scapitis
schromogenes
sdysgalactiae
sepidermidis
serratia
sgallolyticus
shaemolyticus
shewanella
shominis
siniae
sinorhizobium
slugdunensis
smaltophilia
smitis
smutans_Do
smutans_Kakano
soralis
sparasitica
pneumoniae
spseudintermedius
spyogenes
sspp
ssuis
sthermophilus
sthermophilus_2
suberis
szooepidemicus
taylorella
tenacibaculum
tpallidum_Grillova
tpallidum_Pla-Diaz
tpyogenes
tvaginalis
ureaplasma
vcholerae
vibrio
vparahaemolyticus
vtapetis
vvulnificus
wolbachia
xfastidiosa
ypseudotuberculosis
yruckeri

And it doesn't appear. I found this odd as it is listed as a scheme in the MLST repo for version 2.25.0: https://github.com/tseemann/mlst/blob/v2.25.0/db/pubmlst/ecloacae/ecloacae.txt

Is this a known issue? I may try updating the container, but I thought I would check first.

Thanks!

Command used and terminal output

Feb-12 18:20:45.466 [main] DEBUG nextflow.cli.Launcher - $> nextflow run /projects/standard/mdh/shared/software_modules/phoenix/2.2.0/phoenix/main.nf -entry PHOENIX -c /projects/standard/mdh/shared/software_modules/phoenix/2.2.0/phoenix_wrapper.config --input /projects/standard/mdh/shared/PHoeNIx-PhyloPHoeNIx_Validation/Isolates_spriggan_phoenix/E_clo/E_clo_260212_samplesheet.csv --outdir E_clo_260212_out --email  --tmpdir /tmp -ansi-log false -resume
Feb-12 18:20:45.643 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 25.04.3

Relevant files

No response

System information

Nextflow version 25.04.3
Phoenix version 2.2.0
HPC
Slurm
Apptainer

[hkunerth]

Hi!

Just returning to this. Is there a sense of whether this will be resolved in a shorter timeframe or if it is something that's more likely to be incorporated into a full version update?

Either is fine, but given our timeline, I may try to adjust the container myself if it will be a longer term project.

Thanks much!

[nvlachos]

Hi @hkunerth ,
I am sorry about the delay. We have resolved the issue and it will be included in an upcoming hotfix. The exact timing that will happen is a little vague, but shouldn't be too long. We have one more larger thing to finish up fixing and then the release will handle a handful of bugs we had found, including this one.

[hkunerth]

That's great to hear. No worries about the timing - I'll look out for the future release. Thanks for the work on this!

[nvlachos]

Actually, while we wait for the release. If you @hkunerth want to try the dev version (v2.3.0-dev), it has the fix in there and should work as long as you aren't trying to use the updater mode on an old scaffold run.

[hkunerth]

That's great! I'll pull it early next week and let you know if I run into any issues. Thanks for letting me know!