buske / silva Goto Github PK

The server is down. Any prevision of when it will be active again?

I m trying to install silve, and this tool tries to download and unpack unafold-3.8.tar.gz. But the links it is using seems to be not available anymore. Kindly provide the alternative link.

Currently it just crashes farther down the analysis pipeline.

@buske
From the documentation, all data files are based on hg19. May I know the suggested steps to prepare the SILVA databases using GRCh38 and GENCODE annotations?

This is the first time I faced an error with SilVA. Anyone to help me?

`Saving genes to pickled file: /home/martiela/Bioinformatica/SilVA/silva-1.1.1-nofolding/data/refGene.pkl
Traceback (most recent call last):

File "/home/martiela/Bioinformatica/SilVA/silva-1.1.1-nofolding/src/input/synonymous.py", line 843, in
sys.exit(main())

File "/home/martiela/Bioinformatica/SilVA/silva-1.1.1-nofolding/src/input/synonymous.py", line 840, in main
script(*args, **kwargs)

File "/home/martiela/Bioinformatica/SilVA/silva-1.1.1-nofolding/src/input/synonymous.py", line 699, in script
filter_variants(genes, filename, protein_coords=protein_coords)

File "/home/martiela/Bioinformatica/SilVA/silva-1.1.1-nofolding/src/input/synonymous.py", line 635, in filter_variants
pos = int(pos)

ValueError: invalid literal for int() with base 10: '18080854\xc2\xa0'
`

Should probably deal with lines with multiple alleles, currently just take first one

I have just installed silva and ran the

./silva-preprocess TMP example/example.vcf

Iam getting below error
Can you help to fix it
thanks

...
Running: 0_gerp.col
Loading optimized table from: /git/silva/silva-1.1.1/data/gerp.refGene.pkl
Completed: cpg.col
Completed: codon.col
Completed: splice.col
Completed: fas-ess.col
Completed: pesx.col
Completed: ese3.col
Completed: maxent.col
Completed: 0_gerp.col
Running: unafold-50.col
Running: vienna-50.col
Completed: unafold-50.col
Completed: vienna-50.col
Standardizing MAT file according to control data...
Traceback (most recent call last):
  File "/git/silva/silva-1.1.1/src/input/standardize.py", line 134, in <module>
    sys.exit(main())
  File "/git/silva/silva-1.1.1/src/input/standardize.py", line 131, in main
    script(*args, **kwargs)
  File "/git/silva/silva-1.1.1/src/input/standardize.py", line 82, in script
    control_header, control_class_col, control = read_examples(control)
  File "/git/silva/silva-1.1.1/src/input/standardize.py", line 29, in read_examples
    with maybe_gzip_open(filename) as ifp:
  File "/git/silva/silva-1.1.1/lib/python/silva/__init__.py", line 16, in maybe_gzip_open
    return open(filename, *args, **kwargs)
IOError: [Errno 2] No such file or directory: '/git/silva/silva-1.1.1/control/NA10851.mat'

I've been trying to run the models. With the command:
./silva-run | head

I get this error:
Running model 0...
./silva-run: ./test: /usr/bin/Rscript: bad interpreter: No such file or directory

How do I fix this?