
Traceback (most recent call last):

 "/usr/local/lib/python2.7/dist-packages/pyspider/libs/base_handler.py", line 187, in run_task
result = self._run_task(task, response)

 "/usr/local/lib/python2.7/dist-packages/pyspider/libs/base_handler.py", line 166, in _run_task
response.raise_for_status()

 "/usr/local/lib/python2.7/dist-packages/pyspider/libs/response.py", line 183, in raise_for_status
raise http_error
HTTPError: HTTP 599: gnutls_handshake() failed: Handshake failed
Traceback (most recent call last):


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/tools/bin/bcbio_nextgen.py", line 238, in <module>

main(**kwargs)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/tools/bin/bcbio_nextgen.py", line 46, in main

run_main(**kwargs)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 45, in run_main

fc_dir, run_info_yaml)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 89, in _run_toplevel

for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 162, in variant2pipeline

samples = joint.square_off(samples, run_parallel)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/bcbio/variation/joint.py", line 142, in square_off

"vrn_file", ["region", "sam_ref", "config"])


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/split.py", line 38, in grouped_parallel_split_combine

parallel_fn(combine_name, combine_args)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel

return run_multicore(fn, items, config, parallel=parallel)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore

for data in joblib.Parallel(parallel["num_jobs"], batch_size=1, backend="multiprocessing")(joblib.delayed(fn)(*x) for x in items):


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 921, in __call__

if self.dispatch_one_batch(iterator):


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 759, in dispatch_one_batch

self._dispatch(tasks)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 716, in _dispatch

job = self._backend.apply_async(batch, callback=cb)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/joblib/_parallel_backends.py", line 182, in apply_async

result = ImmediateResult(func)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/joblib/_parallel_backends.py", line 549, in __init__

self.results = batch()


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 225, in __call__

for func, args, kwargs in self.items]


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 55, in wrapper

return f(*args, **kwargs)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 292, in concat_variant_files

return vcfutils.concat_variant_files(*args)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/bcbio/variation/vcfutils.py", line 371, in concat_variant_files

out_file = _run_concat_variant_files_gatk4(input_file_list, out_file, config)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/bcbio/variation/vcfutils.py", line 394, in _run_concat_variant_files_gatk4

broad_runner.run_gatk(params)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/bcbio/broad/__init__.py", line 365, in run_gatk

log_error=log_error)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 26, in run

_do_run(cmd, checks, log_stdout, env=env)


 "/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 106, in _do_run

raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; unset JAVA_HOME && export PATH=/export/home/ncit/external/a.mizeranschi/bcbio_nextgen/anaconda/bin:$PATH && gatk --java-options '-Xms454m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=/export/home/ncit/external/a.mizeranschi/automated-VC-test/testingVC-merged/work/bcbiotx/tmptAzZBo' GatherVcfs -I /export/home/ncit/external/a.mizeranschi/automated-VC-test/testingVC-merged/work/joint/platypus-joint/testingVC/testingVC-joint-files.list -O /export/home/ncit/external/a.mizeranschi/automated-VC-test/testingVC-merged/work/bcbiotx/tmpZVfkX1/testingVC-joint.vcf.gz
