Cannot connect to the MHCstab server

Installation Type

Standalone

pVACtools Version / Docker Image

latest edition

Python Version

3.8

Operating System

Linux

Describe the bug

Prompt MHCstab connection reset while running pVACseq. Looks like there's something wrong with their server. Hope to get a new connection address.

How to reproduce this bug

#!/bin/bash -ue
pvacseq run \
    --iedb-install-directory /data2/neoantigen/resources/databases/iedb \
    -t 50 \
    -p sample1_vep_phased.vcf.gz \
    -e1 8,9,10,11 \
    -e2 15,16,17,18,19,20,21,22,23,24,25 \
    --normal-sample-name sample1_normal \
    --tumor-purity 0.51 \
     \
    --netmhc-stab \
    --binding-threshold 500 --top-score-metric median --minimum-fold-change 0.0 --normal-cov 5 --tdna-cov 10 --trna-cov 10 --normal-vaf 0.02 --tdna-vaf 0.25 --trna-vaf 0.25 --expn-val 1 --maximum-transcript-support-level 1 \
    sample1_hc_vep_pick.vcf.gz sample1_tumor HLA-A*24:02 NetMHCpan NetMHCIIpan ./

if [ -e ./MHC_Class_I/sample1_tumor.filtered.tsv ]; then
    mv ./MHC_Class_I/sample1_tumor.filtered.tsv ./MHC_Class_I/sample1_tumor_HLA-A*24:02.filtered.tsv
fi
if [ -e ./MHC_Class_I/sample1_tumor.all_epitopes.tsv ]; then
    mv ./MHC_Class_I/sample1_tumor.all_epitopes.tsv ./MHC_Class_I/sample1_tumor_HLA-A*24:02.all_epitopes.tsv
fi
if [ -e ./MHC_Class_II/sample1_tumor.filtered.tsv ]; then
    mv ./MHC_Class_II/sample1_tumor.filtered.tsv ./MHC_Class_II/sample1_tumor_HLA-A*24:02.filtered.tsv
fi
if [ -e ./MHC_Class_II/sample1_tumor.all_epitopes.tsv ]; then
    mv ./MHC_Class_II/sample1_tumor.all_epitopes.tsv ./MHC_Class_II/sample1_tumor_HLA-A*24:02.all_epitopes.tsv
fi

Input files

No response

Log output

Traceback (most recent call last): File "/opt/conda/lib/python3.8/site-packages/urllib3/connectionpool.py", line 670, in urlopen httplib_response = self._make_request( File "/opt/conda/lib/python3.8/site-packages/urllib3/connectionpool.py", line 381, in _make_request self._validate_conn(conn) File "/opt/conda/lib/python3.8/site-packages/urllib3/connectionpool.py", line 978, in _validate_conn conn.connect() File "/opt/conda/lib/python3.8/site-packages/urllib3/connection.py", line 362, in connect self.sock = ssl_wrapsocket( File "/opt/conda/lib/python3.8/site-packages/urllib3/util/ssl.py", line 386, in ssl_wrap_socket return context.wrap_socket(sock, server_hostname=server_hostname) File "/opt/conda/lib/python3.8/ssl.py", line 500, in wrap_socket return self.sslsocket_class._create( File "/opt/conda/lib/python3.8/ssl.py", line 1040, in _create self.do_handshake() File "/opt/conda/lib/python3.8/ssl.py", line 1309, in do_handshake self._sslobj.do_handshake() ConnectionResetError: [Errno 104] Connection reset by peer

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/opt/conda/lib/python3.8/site-packages/requests/adapters.py", line 439, in send resp = conn.urlopen( File "/opt/conda/lib/python3.8/site-packages/urllib3/connectionpool.py", line 726, in urlopen retries = retries.increment( File "/opt/conda/lib/python3.8/site-packages/urllib3/util/retry.py", line 410, in increment raise six.reraise(type(error), error, _stacktrace) File "/opt/conda/lib/python3.8/site-packages/urllib3/packages/six.py", line 734, in reraise raise value.with_traceback(tb) File "/opt/conda/lib/python3.8/site-packages/urllib3/connectionpool.py", line 670, in urlopen httplib_response = self._make_request( File "/opt/conda/lib/python3.8/site-packages/urllib3/connectionpool.py", line 381, in _make_request self._validate_conn(conn) File "/opt/conda/lib/python3.8/site-packages/urllib3/connectionpool.py", line 978, in _validate_conn conn.connect() File "/opt/conda/lib/python3.8/site-packages/urllib3/connection.py", line 362, in connect self.sock = ssl_wrapsocket( File "/opt/conda/lib/python3.8/site-packages/urllib3/util/ssl.py", line 386, in ssl_wrap_socket return context.wrap_socket(sock, server_hostname=server_hostname) File "/opt/conda/lib/python3.8/ssl.py", line 500, in wrap_socket return self.sslsocket_class._create( File "/opt/conda/lib/python3.8/ssl.py", line 1040, in _create self.do_handshake() File "/opt/conda/lib/python3.8/ssl.py", line 1309, in do_handshake self._sslobj.do_handshake() urllib3.exceptions.ProtocolError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/opt/conda/bin/pvacseq", line 8, in sys.exit(main()) File "/opt/conda/lib/python3.8/site-packages/pvactools/tools/pvacseq/main.py", line 123, in main args[0].func.main(args[1]) File "/opt/conda/lib/python3.8/site-packages/pvactools/tools/pvacseq/run.py", line 138, in main pipeline.execute() File "/opt/conda/lib/python3.8/site-packages/pvactools/lib/pipeline.py", line 484, in execute PostProcessor(*post_processing_params).execute() File "/opt/conda/lib/python3.8/site-packages/pvactools/lib/post_processor.py", line 64, in execute self.call_netmhc_stab() File "/opt/conda/lib/python3.8/site-packages/pvactools/lib/post_processor.py", line 225, in call_netmhc_stab NetMHCStab(self.net_chop_fh.name, self.netmhc_stab_fh.name, self.file_type, self.top_score_metric).execute() File "/opt/conda/lib/python3.8/site-packages/pvactools/lib/netmhc_stab.py", line 37, in execute alleles = self.valid_alleles(list(set(observed_alleles).intersection(set(mhci_alleles)))) File "/opt/conda/lib/python3.8/site-packages/pvactools/lib/netmhc_stab.py", line 195, in valid_alleles response = self.query_netmhcstabpan_server(staging_file, 9, allele.replace("", "")) File "/opt/conda/lib/python3.8/site-packages/pvactools/lib/netmhc_stab.py", line 152, in query_netmhcstabpan_server response = requests.post( File "/opt/conda/lib/python3.8/site-packages/requests/api.py", line 119, in post return request('post', url, data=data, json=json, kwargs) File "/opt/conda/lib/python3.8/site-packages/requests/api.py", line 61, in request return session.request(method=method, url=url, kwargs) File "/opt/conda/lib/python3.8/site-packages/requests/sessions.py", line 530, in request resp = self.send(prep, send_kwargs) File "/opt/conda/lib/python3.8/site-packages/requests/sessions.py", line 643, in send r = adapter.send(request, kwargs) File "/opt/conda/lib/python3.8/site-packages/requests/adapters.py", line 498, in send raise ConnectionError(err, request=request) requests.exceptions.ConnectionError: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))

Output files

No response

griffithlab / pVACtools