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hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation
MIT License
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Inconsistent behavior with lumpyexpress #108

Open rajeha opened 7 years ago

rajeha commented 7 years ago

I had an error running Lumpy through Speedseq, but the problem was resolved using Lumpy directly. Maybe your version of Lumpy is out of date? I think it has to do with many reads being filtered by paired_distro.py.

Speedseq:

$ speedseq sv  -B ../bwa/bwa.sorted.bam -S ../bwa/bwa.sorted.splitters.bam -D ../bwa/bwa.sorted.discordants.bam -R ../../ref/s.pombe.fasta -o lumpy

Sourcing executables from /home/rajeha/bin/speedseq/bin/speedseq.config ...

Checking for required python modules (/usr/bin/python2.7)... create temporary directory

Running LUMPY express Sourcing executables from /home/rajeha/bin/speedseq/bin/speedseq.config ...

Checking for required python modules (/usr/bin/python2.7)... create temporary directory Calculating insert distributions... Library read groups: id Library read length: 251 /home/rajeha/.local/lib/python2.7/site-packages/numpy/core/fromnumeric.py:2889: RuntimeWarning: Mean of empty slice. out=out, **kwargs) /home/rajeha/.local/lib/python2.7/site-packages/numpy/core/_methods.py:80: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount) Traceback (most recent call last): File "/home/rajeha/bin/speedseq//bin/pairend_distro.py", line 106, in (removed, upper_cutoff)) TypeError: %d format: a number is required, not numpy.float64

Lumpy:

$ lumpyexpress -B ../bwa/bwa.sorted.bam -S ../bwa/bwa.sorted.splitters.bam -D ../bwa/bwa.sorted.discordants.bam -o lumpy

Sourcing executables from /home/rajeha/bin/lumpy-sv/scripts/lumpyexpress.config ...

Checking for required python modules (/usr/bin/python)... Calculating insert distributions... Library read groups: id Library read length: 251 Warning: only 0 elements in distribution (min: 1000) done 0 Running LUMPY... I 1000000 II 1000000 III 1000000 LUMPY Express done