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deeptools / deepTools

Tools to process and analyze deep sequencing data.
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"502 Proxy Error" when using bigwigCompare #1308

Closed Reb08 closed 7 months ago

Reb08 commented 7 months ago

Good morning,

I am working with ChIP-seq data. I have two replicates per sample. I am creating a coverage file for each replicate using bamCoverage, merging the two resulting .bw files using bigWigMerge, sorting the file and then obtaining the final merged .bw file using bedGraphToBigWig. I would now like to subtract the input from the merged sample using bigwigCompare. I have been using the following code:

bigwigCompare -b1 {merged.bw sample file} -b2 {input.bw file} --operation subtract -o {output.bw file} --numberOfProcessors max

However, I keep getting the following error:

"Traceback (most recent call last): File "/services/tools/deeptools/3.5.2/bin/bigwigCompare", line 12, in main(args) File "/services/tools/deeptools/3.5.2/lib/python3.10/site-packages/deeptools/bigwigCompare.py", line 144, in main foo = db.deepBlue(deepBlueFiles[0][0], url=args.deepBlueURL, userKey=args.userKey) File "/services/tools/deeptools/3.5.2/lib/python3.10/site-packages/deeptools/deepBlue.py", line 138, in init experimentID = self.getEID() File "/services/tools/deeptools/3.5.2/lib/python3.10/site-packages/deeptools/deepBlue.py", line 164, in getEID (status, resps) = self.server.search(self.sample, "experiments", self.userKey) File "/services/tools/deeptools/3.5.2/lib/python3.10/xmlrpc/client.py", line 1122, in call return self.send(self.name, args) File "/services/tools/deeptools/3.5.2/lib/python3.10/xmlrpc/client.py", line 1464, in request response = self.transport.request( File "/services/tools/deeptools/3.5.2/lib/python3.10/xmlrpc/client.py", line 1166, in request return self.single_request(host, handler, request_body, verbose) File "/services/tools/deeptools/3.5.2/lib/python3.10/xmlrpc/client.py", line 1196, in single_request raise ProtocolError( xmlrpc.client.ProtocolError: <ProtocolError for deepblue.mpi-inf.mpg.de/xmlrpc: 502 Proxy Error>"

(deeptools --version: deeptools 3.5.2; python --version: Python 3.10.11)

Any idea what could be causing this and how to fix it?

Thank you

WardDeb commented 7 months ago

This implies your input files (b1, b2 or both) are not specified correctly. The deepblue support is dropped from 3.5.5 onwards (and thus the error would be more meaningful there).