Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Output scaffolds_FINAL.fasta is binary #174

Open
mkyriak opened this issue Aug 15, 2023 · 0 comments
Open

Output scaffolds_FINAL.fasta is binary #174

mkyriak opened this issue Aug 15, 2023 · 0 comments

Comments

@mkyriak
Copy link

mkyriak commented Aug 15, 2023

Hello!

I recently installed salsa using mamba in the following environment:
`# packages in environment at salsa2:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
agptools 0.0.1 pypi_0 pypi
bedtools 2.31.0 hf5e1c6e_2 bioconda
boost-cpp 1.74.0 h75c5d50_8 conda-forge
bz2file 0.98 pypi_0 pypi
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2023.7.22 hbcca054_0 conda-forge
certifi 2019.11.28 py27h8c360ce_1 conda-forge
decorator 4.4.2 py_0 conda-forge
icu 70.1 h27087fc_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-ng 13.1.0 he5830b7_0 conda-forge
libgomp 13.1.0 he5830b7_0 conda-forge
libsqlite 3.42.0 h2797004_0 conda-forge
libstdcxx-ng 13.1.0 hfd8a6a1_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
ncurses 6.4 hcb278e6_0 conda-forge
networkx 1.11 py27_0 conda-forge
openssl 1.1.1v hd590300_0 conda-forge
pip 20.1.1 pyh9f0ad1d_0 conda-forge
pyfaidx 0.7.1 pypi_0 pypi
python 2.7.15 h5a48372_1011_cpython conda-forge
python_abi 2.7 1_cp27mu conda-forge
readline 8.2 h8228510_1 conda-forge
salsa2 2.3 py27h16ec135_1 bioconda
screed 1.0.4 pypi_0 pypi
setuptools 44.0.0 py27_0 conda-forge
six 1.16.0 pypi_0 pypi
sqlite 3.42.0 h2c6b66d_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.2 hfc55251_7 conda-forge`

I managed to run salsa, but the scaffolds_FINAL.fasta seems to be a binary file. Is there any way to generate the fasta with the actual sequences?

Thank you in advance for your time and help!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant