Samtools problem with running (Conda)

Question

[misterie]

Hi,

I have a problem with running Samtools and other software installed by Conda. Every times I get:

dyld: Symbol not found: _stdscr
  Referenced from: /Users/bart/miniconda3/bin/samtools
  Expected in: /Users/bart/miniconda3/bin/../lib/libncursesw.6.dylib
 in /Users/bart/miniconda3/bin/samtools
Abort trap: 6

How can I fix it? I have tried to reinstall Openssl but I did not help me.

[Pierre Lindenbaum]

related ?

It's now a month since I opened a pull request to fix Conda's ncurses libraries, at their request. No response yet other than “we don't have the expertise to review your PR”. If you actually use #Conda, you might like to encourage them to look at this fix! https://t.co/vzDeLK7oEP

— John Marshall (@jomarnz) October 10, 2018

[misterie]

Might be, but two days ago everything was fine. After installation a few (pbalign Canu) extra softwares the problem occurs. I tried to uninstall those programs, but the problem is still visible.

[ATpoint]

Try this, which helped me in a similar situation:

conda remove samtools
conda install -c conda-forge curl
conda install -c bioconda --freeze-installed samtools

From there on, always use --freeze-installed to avoid up/downgrading depending on channel.

[Devon Ryan]

Are you using conda 4.6? The 4.5 releases don't have a --freeze-installed option.

[misterie]

I am using Miniconda3 latest version from https://conda.io/en/latest/miniconda.html

[ATpoint]

conda --version is what you should tell us. If not conda 4.6, then it is probably --no-update-dependencies

[sabhi90]

Create a new environment with anaconda:

conda create --name Env1 samtools
Conda activate Env1

Now it should let you run samtools without the dependencies

Answer 1

[steve]

I have had issues with ncurses giving similar errors with other programs, the solution was to install ncurses from the conda-forge channel before installing the rest of the dependencies;

conda install -y conda-forge::ncurses
conda install -y -c bioconda samtools

Maybe give this a shot. I would recommend testing it in a fresh conda installation, or an env, as Devon says

Another troubleshooting tactic might be to look up which versions of samtools are available, and just start decrementing the version number until you find one that works.

[hliang]

works for me on conda 4.7.5, macOS high sierra 10.13.4

[Marco Pannone]

Works for me as well after running conda remove samtools. MacOS Catalina v10.15.3

Answer 2

[Devon Ryan]

Avoid directly using conda install as much as possible as this is a wonderful way of breaking already installed programs (use environments). If you must (or really want to) use conda install, ensure you specify --no-update-dependencies.

The easiest fix is to create a new environment with samtools. The longer solution is to figure out what was upgraded and downgrade it.

[steve]

Avoid directly using conda install as much as possible

A nice workaround to this is to just have a dedicated conda installation for every software stack, and keep the entire installation saved in a script for reproducibility :) Example here

[Devon Ryan]

I assume you mean a dedicated environment, since a dedicated conda installation would be rather wasteful.

[steve]

No, definitely a full dedicated installation. Its only wasteful if you care about disk space. Its a much more portable and reproducible method than just assuming the target system will have a compatible conda version already installed. Almost like a self-contained Docker replacement minus the requirement for admin access

[misterie]

Ok, thank you. I also tried to uninstall conda and remove all packages, but it did not solve my problem. Sometimes I get problem like that:

dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib
Referenced from: /Users/bart/miniconda3/bin/samtools
Reason: image not found
Abort trap: 6

[Devon Ryan]

Odds are that that's from openssl (if so, you're the 3rd person this week to get bitten by this), so try conda install openssl=1.0.2p

[misterie]

still the same problem. I have tried to make a link in some directory associated with *.dylib files or copy between directories.

Now I tried to install openssl=1.0.2p but still:

dyld: Symbol not found: _stdscr
Referenced from: /Users/bart/miniconda3/bin/samtools
 Expected in: /Users/bart/miniconda3/bin/../lib/libncursesw.6.dylib
 in /Users/bart/miniconda3/bin/samtools
 Abort trap: 6

[Devon Ryan]

Then it upgraded ncurses on you too, so conda install --no-update-dependencies ncurses=6.1. Really you should just make a new environment though.