ERROR in lumpyexpress -n: command not found; [: ==: unary operator expected

[ClarenceHsiang]

Dear LUMPY-SV team,
Good evening.
When I ran lumpyexpress, I got this message below,
Please give me some suggestions or solutions.

Thank you so much

Clarence

Checking for required python modules (/home/hsiang/miniconda3/envs/Python2_7/bin/python)...
/home/hsiang/miniconda3/envs/Python2_7/bin/lumpyexpress: line 15: -n: command not found
/home/hsiang/miniconda3/envs/Python2_7/bin/lumpyexpress: line 16: [: ==: unary operator expected
Calculating insert distributions...
Library read groups: id
Library read length: 150
Removed 1314 outliers with isize >= 781
done
79

[cyclovecqh]

I also faced this problem.I hope someone can answer it.

[goeckeritz]

Anyone have luck on this issue? I'm also having this problem -- installed it via conda:

conda install -c "bioconda/label/cf201901" lumpy-sv

But had to load Sambamba and samblaster separately on our hpcc system since those didn't install properly.

Hopefully solving this error will give me some calls - right now, all of the genotypes are simply ./.

[ryanlayer]

This is typically either a python issue or that your system does not have
hexdump.

See #256

I would recommend using the latest lumpy wrapper, smoove.

https://github.com/brentp/smoove

[reminder098]

I solved this problem for several hours today.
In a word ,you need to add HEXDUMP=`which hexdump || true` in your lumpyexpress.config file.
The path of this file can be found when you run lumpyexpress's log(like :Sourcing executables from /opt/conda/envs/py2.7/bin/lumpyexpress.config).

For the reason:
A function called source_binaries() in .../bin/lumpyexpress has conditional statement,which cause this problem.
When you sourcing executables from its config file,the $HEXDUMP is a null value.
But if you sourcing excutables from its auto-source mode by another condition,this problem will not occur.

[Canglan111]

I solved this problem for several hours today. In a word ,you need to add HEXDUMP=which hexdump || true in your lumpyexpress.config file. The path of this file can be found when you run lumpyexpress's log(like :Sourcing executables from /opt/conda/envs/py2.7/bin/lumpyexpress.config).

For the reason: A function called source_binaries() in .../bin/lumpyexpress has conditional statement,which cause this problem. When you sourcing executables from its config file,the $HEXDUMP is a null value. But if you sourcing excutables from its auto-source mode by another condition,this problem will not occur.

Thank you very much. I solved this problem!