Comments (2)
Please suggest how to get around this error?
from cenote-taker2.
Hi JSSaini,
Thanks for raising this issue. I apologize for the long delay in responding. I was unable to respond to github issues for a several weeks.
Regarding fastpathz
, there was a previous user who seemed to have a similar problem #3 , and they resolved it by directly installing fastpath
conda activate cenote-taker2_env
pip install fastpath
Let me know if this helps.
Your issues that appear to involve "blastx.tab" files and Entrez Direct
are likely an issue caused by improper set up of the krona database, as in issue #22
To fix this, change to the main Cenote-Taker 2
directory and use these commands (This requires at least 4 CPUs for some reason and will take 20-40 minutes, so please have those resources available):
KRONA_DIR=$( which python | sed 's/bin\/python/opt\/krona/g' )
cd ${KRONA_DIR}
sh updateTaxonomy.sh
cd ${KRONA_DIR}
sh updateAccessions.sh
If you are able to complete this fixes, please test on a small dataset, such as the DNA test contigs provided with the script, and send me the log file and a zipped directory of the output.
Best,
Mike
from cenote-taker2.
Related Issues (20)
- Getting phage contigs even after "phage pruning" is set to true HOT 3
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- erro:grep: sequin directory/*.fsa: No such file or directory when using latest cenote-Taker2.0.1 HOT 2
- BlastN "no high coverage hits HOT 3
- DTR removing HOT 1
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- cenote-taker2 vs (blastn nt & diamond nr) HOT 1
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- DTR HOT 3
- ResolvePackageNotFound: - bbtools=37.62 HOT 1
- replace tbl2asn with table2asn
- ValueError: unsupported format character 'I' (0x49) at index 66 HOT 3
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- ERROR: Invalid inference value tRNAscan-SE HOT 1
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from cenote-taker2.