urllib2.HTTPError: HTTP Error 414: Request-URI Too Large

[tramaraj]

Hi -

I am trying to use the script kt_summarize.py to plot Kraken output with Krona. For some kraken report files it works fine, but from some kraken output files I get the following error message,

python ktoolu/kt_summarize.py --draw-krona-plot KRONA_PLOT.html --path-to-krona kronatools/KronaTools-2.6/bin/ --write-summary KRONA_SUMMARY kraken-report.txt
Traceback (most recent call last):
File "ktoolu/kt_summarize.py", line 122, in
if name == 'main': main()
File "ktoolu/kt_summarize.py", line 81, in main
taxInfoDict = {tinfo['TaxId']: [tinfo, taxCounter[tinfo['TaxId']]] for tinfo in fetchTaxonomyData(taxids)}
File "ktoolu/kt_summarize.py", line 38, in fetchTaxonomyData
handle = Entrez.efetch(db='Taxonomy', id=','.join(ids), retmode='xml')
File "/sw/python/2.7.1/lib/python2.7/site-packages/Bio/Entrez/init.py", line 139, in efetch
return _open(cgi, variables)
File "/sw/python/2.7.1/lib/python2.7/site-packages/Bio/Entrez/init.py", line 455, in _open
raise exception
urllib2.HTTPError: HTTP Error 414: Request-URI Too Large

Any thoughts on how to get this rectified.

Thank You.
TR

[cschu]

Hi TR

do you maybe have a lot of tax ids in your output? That could explain
it, as kt_summarize.py communicates with NCBI-Taxonomy to obtain
taxonomy labels. In that case it is clearly a bug and I need to put some
time into fixing it. Could you provide me the kraken classification file
by chance?

Sorry about the bug.

Best
Christian

On 21/12/15 19:03, Thiru Ramaraj wrote:

Hi -

I am trying to use the script kt_summarize.py to plot Kraken output
with Krona. For some kraken report files it works fine, but from some
kraken output files I get the following error message,

python ktoolu/kt_summarize.py --draw-krona-plot KRONA_PLOT.html
--path-to-krona kronatools/KronaTools-2.6/bin/ --write-summary
KRONA_SUMMARY kraken-report.txt
Traceback (most recent call last):
File "ktoolu/kt_summarize.py", line 122, in
if name == 'main': main()
File "ktoolu/kt_summarize.py", line 81, in main
taxInfoDict = {tinfo['TaxId']: [tinfo, taxCounter[tinfo['TaxId']]] for
tinfo in fetchTaxonomyData(taxids)}
File "ktoolu/kt_summarize.py", line 38, in fetchTaxonomyData
handle = Entrez.efetch(db='Taxonomy', id=','.join(ids), retmode='xml')
File
"/sw/python/2.7.1/lib/python2.7/site-packages/Bio/Entrez/init.py",
line 139, in efetch
return /open(cgi, variables)
File
"/sw/python/2.7.1/lib/python2.7/site-packages/Bio/Entrez/_init/.py",
line 455, in _open
raise exception
urllib2.HTTPError: HTTP Error 414: Request-URI Too Large

Any thoughts on how to get this rectified.

Thank You.
TR

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