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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Lumpy bamlibs.py error #307

Open nelsonchanhk opened 5 years ago

nelsonchanhk commented 5 years ago

Hello,

I've tried lumpy-sv from conda. However, it has the following error. I have NumPy, pysam, hexdump and bamkit installed. Below is the input/output. Please kindly help. Thank you!

lumpyexpress -B HA1.bam -S HA1.splitters.bam -D HA1.discordants.bam -o HA1.vcf Sourcing executables from /home/nelson/miniconda3/envs/bioinfo/bin/lumpyexpress.config ...

Checking for required python modules (/home/nelson/miniconda3/envs/bioinfo/bin/python)... /home/nelson/miniconda3/envs/bioinfo/bin/lumpyexpress: line 15: -n: command not found /home/nelson/miniconda3/envs/bioinfo/bin/lumpyexpress: line 16: [: ==: unary operator expected /home/nelson/miniconda3/envs/bioinfo/bin/python: can't open file '/home/nelson/miniconda3/envs/bioinfo/bin/scripts/bamkit/bamlibs.py': [Errno 2] No such file or directory

tyyiyi commented 5 years ago

I also have the same problem, have you solved it?

ryanlayer commented 5 years ago

I recommend that you use the new lumpy wrapper smoove https://github.com/brentp/smoove

On Jun 22, 2019, at 9:08 AM, tyyiyi notifications@github.com wrote:

I also have the same problem, have you solved it?

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ryanlayer commented 5 years ago

I recommend that you use the new lumpy wrapper smoove https://github.com/brentp/smoove

On Jun 7, 2019, at 9:41 AM, nelsonchanhk notifications@github.com wrote:

Hello,

I've tried lumpy-sv from conda. However, it has the following error. I have NumPy, pysam, hexdump and bamkit installed. Below is the input/output. Please kindly help. Thank you!

lumpyexpress -B HA1.bam -S HA1.splitters.bam -D HA1.discordants.bam -o HA1.vcf Sourcing executables from /home/nelson/miniconda3/envs/bioinfo/bin/lumpyexpress.config ...

Checking for required python modules (/home/nelson/miniconda3/envs/bioinfo/bin/python)... /home/nelson/miniconda3/envs/bioinfo/bin/lumpyexpress: line 15: -n: command not found /home/nelson/miniconda3/envs/bioinfo/bin/lumpyexpress: line 16: [: ==: unary operator expected /home/nelson/miniconda3/envs/bioinfo/bin/python: can't open file '/home/nelson/miniconda3/envs/bioinfo/bin/scripts/bamkit/bamlibs.py': [Errno 2] No such file or directory

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.