error

[vicru93]

Hi, I'm having trouble running the workflow as instructed by the tool.
This is my command line used:

nextflow run /hpcfs/home/ing_quimica/v.rua/mettannotator -profile singularity --input /hpcfs/home/ing_quimica/v.rua/Binning_DA/BOVINAZA/Binning_A2_Bovinaza/Final_bestbinset/binsFiltrados/BAT_results/out_mettannotatorA2/assemblies_sheet.csv --outdir /hpcfs/home/ing_quimica/v.rua/Binning_DA/BOVINAZA/Binning_A2_Bovinaza/Final_bestbinset/binsFiltrados/BAT_results/out_mettannotatorA2 --dbs /hpcfs/home/ing_quimica/v.rua/mettanotatorDB --bakta

This is the directory with the bins for my analysis:
ls
BAT_results bin13_IDBA_re-assembly_contigs.fa bin3_SPAdes_re-assembly_contigs.fa bin6_IDBA_re-assembly_contigs.fa
bin11_SPAdes_re-assembly_contigs.fa bin17_SPAdes_re-assembly_contigs.fa bin4_SPAdes_re-assembly_contigs.fa bin8_SPAdes_re-assembly_contigs.fa
bin12.fa bin18.fa bin5.fa bin9_SPAdes_re-assembly_contigs.fa

And finally, this is my .csv file:

head -n 20 assemblies_sheet.csv
prefix,assembly,taxid
bin11,/hpcfs/home/ing_quimica/v.rua/Binning_DA/BOVINAZA/Binning_A2_Bovinaza/Final_bestbinset/binsFiltrados/bin11_SPAdes_re-assembly_contigs.fa,2021373
bin12,/hpcfs/home/ing_quimica/v.rua/Binning_DA/BOVINAZA/Binning_A2_Bovinaza/Final_bestbinset/binsFiltrados/bin12.fa,2762215
bin13,/hpcfs/home/ing_quimica/v.rua/Binning_DA/BOVINAZA/Binning_A2_Bovinaza/Final_bestbinset/binsFiltrados/bin13_IDBA_re-assembly_contigs.fa,1868793
bin17,/hpcfs/home/ing_quimica/v.rua/Binning_DA/BOVINAZA/Binning_A2_Bovinaza/Final_bestbinset/binsFiltrados/bin17_SPAdes_re-assembly_contigs.fa,1872421
bin18,/hpcfs/home/ing_quimica/v.rua/Binning_DA/BOVINAZA/Binning_A2_Bovinaza/Final_bestbinset/binsFiltrados/bin18.fa,2005355
bin3,/hpcfs/home/ing_quimica/v.rua/Binning_DA/BOVINAZA/Binning_A2_Bovinaza/Final_bestbinset/binsFiltrados/bin3_SPAdes_re-assembly_contigs.fa,2027871
bin4,/hpcfs/home/ing_quimica/v.rua/Binning_DA/BOVINAZA/Binning_A2_Bovinaza/Final_bestbinset/binsFiltrados/bin4_SPAdes_re-assembly_contigs.fa,2030927
bin5,/hpcfs/home/ing_quimica/v.rua/Binning_DA/BOVINAZA/Binning_A2_Bovinaza/Final_bestbinset/binsFiltrados/bin5.fa,1810932
bin6,/hpcfs/home/ing_quimica/v.rua/Binning_DA/BOVINAZA/Binning_A2_Bovinaza/Final_bestbinset/binsFiltrados/bin6_IDBA_re-assembly_contigs.fa,2908840
bin8,/hpcfs/home/ing_quimica/v.rua/Binning_DA/BOVINAZA/Binning_A2_Bovinaza/Final_bestbinset/binsFiltrados/bin8_SPAdes_re-assembly_contigs.fa,83614
bin9,/hpcfs/home/ing_quimica/v.rua/Binning_DA/BOVINAZA/Binning_A2_Bovinaza/Final_bestbinset/binsFiltrados/bin9_SPAdes_re-assembly_contigs.fa,1950483

---

my out:
nextflow.log

[vicru93]

This was the configuration used for the HPC:

srun --mem=100G --pty bash -i
module load nextflow/23.04.1
module load singularity/3.7.1

[mberacochea]

Hi @vicru93,

Thank you for reporting the issue. We haven't encountered that one on our side, but it seems to be related to Singularity and CRISPRCasFinder.

I'm investigating the issue to come up with a fix or workaround. In the meantime, could you try running the pipeline with a more recent version of Singularity (if available in your HPC cluster)?

Cheers

[vicru93]

Hi, I have already updated NextFlow and Singularity to the latest available versions, it still gives me an error, I attach the .log file of the executed process.

Best w.

Victor.

nextflow.log

[mberacochea]

Hi @vicru93,

Alright, the error is exactly the same. I can't reproduce this on my side. Do you think you can upload the assembly "bin18" for me to test on my side?.

Cheers

[mberacochea]

As a side note, you can run the pipeline using Slurm (you would need to create/adjust a profile for your cluster). I can give you a hand with it.

[vicru93]

Hi @mberacochea:

I had to run everything on my PC and the error disappeared, I guess because I had "sudo" on my PC I was able to install and everything worked with docker (in the cluster I had the problem because I didn't have "sudo" adm permissions for the singularity installation, which was broken and I couldn't even install docker).

Right now I'm running my first test, my PC has 24 GB RAM and 8 cores, so I think it's perfect to run mettannotator locally.
I guess this will take some more time :(

I'll let you know how it goes in the next few days, I hope to have good results, this is a great tool for what I want to do with my research.

Best wishes,

Victor.

[mberacochea]

I'm closing this one, please re-open it if needed