Open ClarenceHsiang opened 1 year ago
I also faced this problem.I hope someone can answer it.
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 ./.
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.
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.
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!
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