Question: Samtools problem with running (Conda)
1
gravatar for misterie
12 months ago by
misterie90
misterie90 wrote:

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.

conda samtools • 2.6k views
ADD COMMENTlink modified 7 months ago by steve2.4k • written 12 months ago by misterie90

related ?

ADD REPLYlink modified 12 months ago • written 12 months ago by Pierre Lindenbaum126k

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.

ADD REPLYlink written 12 months ago by misterie90

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.

ADD REPLYlink written 12 months ago by ATpoint30k

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

ADD REPLYlink written 12 months ago by Devon Ryan94k

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

ADD REPLYlink written 12 months ago by misterie90

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

ADD REPLYlink written 12 months ago by ATpoint30k

Create a new environment with anaconda:

conda create --name Env1 samtools
Conda activate Env1

Now it should let you run samtools without the dependencies

ADD REPLYlink written 7 months ago by sabhi900
1
gravatar for Devon Ryan
12 months ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

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.

ADD COMMENTlink modified 12 months ago • written 12 months ago by Devon Ryan94k

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
ADD REPLYlink modified 12 months ago • written 12 months ago by misterie90
1

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

ADD REPLYlink written 12 months ago by Devon Ryan94k

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
ADD REPLYlink written 12 months ago by misterie90
1

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.

ADD REPLYlink modified 12 months ago • written 12 months ago by Devon Ryan94k

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

ADD REPLYlink modified 7 months ago • written 7 months ago by steve2.4k

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

ADD REPLYlink written 7 months ago by Devon Ryan94k

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

ADD REPLYlink written 7 months ago by steve2.4k
1
gravatar for steve
7 months ago by
steve2.4k
United States
steve2.4k wrote:

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.

ADD COMMENTlink modified 7 months ago • written 7 months ago by steve2.4k

works for me on conda 4.7.5, macOS high sierra 10.13.4

ADD REPLYlink written 7 months ago by hliang100
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