Error running Clairvoyante callVarBam

[Peter Edge]

I get the following error running Clairvoyante callVarBam:

clairvoyante.py callVarBam        --chkpnt_fn trainedModels/fullv3-pacbio-ngmlr-hg002-hg19/learningRate1e-3.epoch999        --ref_fn data/genomes/hg19.fa        --bam_fn data/NA12878.1000g/aligned_reads/pacbio/pacbio.blasr.all.44x.bam        --ctgName chr20        --ctgStart 1000000        --ctgEnd 2000000        --call_fn extra_data/NA12878.1000g/variants/clairvoyante.pacbio.blasr.44x.unfiltered/20.vcf.tmp        --sampleName NA24385        --threshold 0.125        --minCoverage 4        --threads 4

Delay 3 seconds before starting variant calling ...
sched_setaffinity: Invalid argument
failed to set pid 0's affinity.
callVar.py exited with exceptions. Exiting...
samtools view: writing to standard output failed: Broken pipe
Traceback (most recent call last):
  File "/home/pedge/git/longshot_study/scripts/.snakemake.q3qx79aq.clairvoyante.py", line 60, in <module>
    assert(s==0)
AssertionError
samtools view: error closing standard output: -1
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1

[Peter Edge]

I was able to resolve this by forcing taskSet to be "" in callVarBam.py

[Ruibang Luo]

Great! Please refer to #11 and #20 for some previous discussions.