search

GenomicsAotearoa / metagenomics_summer_school

Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
https://genomicsaotearoa.github.io/metagenomics_summer_school/
GNU General Public License v3.0
53 stars 30 forks source link

Viral taxonomy - cytoscape prep (appendix (ex11)) #86

Closed kmhandley closed 3 months ago

kmhandley commented 3 months ago

module load Singularity/3.11.3 \ MCL/14.137-gimkl-2020a \ DIAMOND/2.1.9-GCC-11.3.0

Error message:

There are messages associated with the following module(s):

Singularity/3.11.3: Warning: Singularity is deprecated at NeSI, please switch to using Apptainer instead.

kmhandley commented 3 months ago

Second error message after running:

singularity run $container/vcontact2.simg \ vcontact2_gene2genome --proteins viral_taxonomy/checkv_combined.faa \ --output viral_taxonomy/viral_genomes_g2g.csv \ -s 'Prodigal-FAA'

ERROR: /opt/conda/bin/vcontact2_gene2genome:174: DeprecationWarning: 'U' mode is deprecated with open(results.proteins, 'rU') as proteins_fh: Traceback (most recent call last): File "/opt/conda/bin/vcontact2_gene2genome", line 174, in with open(results.proteins, 'rU') as proteins_fh: FileNotFoundError: [Errno 2] No such file or directory: 'viral_taxonomy/checkv_combined.faa'

NOTE: file exists. ls viral_taxonomy/checkv_combined.faa viral_taxonomy/checkv_combined.faa

DininduSenanayake commented 3 months ago

Singularity/3.11.3: Warning: Singularity is deprecated at NeSI, please switch to using Apptainer instead.

Fixed in https://github.com/GenomicsAotearoa/metagenomics_summer_school/commit/36ff679b812ece6e1199368bf85433a358ac4747

JSBoey commented 3 months ago