computeMatrix-- socket.gaierror: [Errno -2] Name or service not known

[ryanmboileau]

Hello deeptools!

I am running into an error while attempting to computeMatrix. I am using deeptools 3.5.1 and Python 3.7.6. Although my input bigwigs are processed similarly there seems to be issues with certain samples i.e. it runs fine if I remove these samples.

Ideas? I would like to generate heatmaps for all of my samples and more. Thanks!

Input

computeMatrix reference-point \ --referencePoint center \ --regionsFileName ${REGIONS} \ --scoreFileName CT1_Naive_R1_H3K27ac.espike.gt130.ignXMY.e.bw CT1_Form_R1_H3K27ac.espike.gt130.ignXMY.e.bw CT1_Naive_DKO_H3K27ac.espike.gt130.ignXMY.e.bw \ CT1_Form_DKO_H3K27ac.espike.gt130.ignXMY.e.bw Naive.mRp.clN.bigWig Form.mRp.clN.bigWig Naive_H3K4m3.mRp.clN.bigWig Formative_H3K4m3.mRp.clN.bigWig \ Naive_H3K27ac_R1.bigWig Naive_H3K27ac_R2.bigWig Form_H3K27ac_R1.bigWig Form_H3K27ac_R2.bigWig Naive_H3K27ac.mRp.clN.bigWig Form_H3K27ac.mRp.clN.bigWig \ --outFileName ${OUTDIR}/${analysisname}.${uniqueid}.gz \ --outFileSortedRegions ${OUTDIR}/${analysisname}.sortedregions.${uniqueid}.bed \ -b 2500 \ -a 2500 \ --missingDataAsZero \ -p 1 \ --binSize 20 \ --sortRegions descend \ --sortUsing mean \ <

Resulting output:

Preloading the following deepBlue files: Form_H3K27ac.mRp.clN.bigWig Traceback (most recent call last): File "/c4/home/rboileau/miniconda3/envs/epigenomics/bin/computeMatrix", line 14, in main(args) File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/site-packages/deeptools/computeMatrix.py", line 412, in main res = list(map(db.preloadWrapper, deepBlueFiles)) File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/site-packages/deeptools/deepBlue.py", line 114, in preloadWrapper res = deepBlue(foo[0], url=args.deepBlueURL, userKey=args.userKey) File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/site-packages/deeptools/deepBlue.py", line 138, in init experimentID = self.getEID() File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/site-packages/deeptools/deepBlue.py", line 164, in getEID (status, resps) = self.server.search(self.sample, "experiments", self.userKey) File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/xmlrpc/client.py", line 1112, in call return self.send(self.name, args) File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/xmlrpc/client.py", line 1452, in request verbose=self.verbose File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/xmlrpc/client.py", line 1154, in request return self.single_request(host, handler, request_body, verbose) File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/xmlrpc/client.py", line 1166, in single_request http_conn = self.send_request(host, handler, request_body, verbose) File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/xmlrpc/client.py", line 1279, in send_request self.send_content(connection, request_body) File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/xmlrpc/client.py", line 1309, in send_content connection.endheaders(request_body) File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/http/client.py", line 1247, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/http/client.py", line 1026, in _send_output self.send(msg) File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/http/client.py", line 966, in send self.connect() File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/http/client.py", line 938, in connect (self.host,self.port), self.timeout, self.source_address) File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/socket.py", line 707, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): File "/c4/home/rboileau/miniconda3/envs/epigenomics/lib/python3.7/socket.py", line 752, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): socket.gaierror: [Errno -2] Name or service not known <

[dpryan79]

Given the error, it seems there's a typo in one of the file names. It's trying to retrieve at least one file from deepBlue rather than the local file system.

[ryanmboileau]

Thank you-- hidden special characters were the cause of the issue.

[dpryan79]

Ah, those will get you every time.