AssertionError when running sourmash-lca #597
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I install again this software used conda,and the same problem appear: Traceback (most recent call last):ca.json.gz |
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aiee you are running into a problem where we have implemented new functionality
for LCA databases, but not officially released the new code that uses them --
it's on the master branch on github, but not yet in bioconda or on pypi!
my apologies.
may I ask where you are downloading the databases from?
best,
--titus
p.s. the error message in the new version of sourmash is much clearer! oops.
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Thank you very much!Jsut now I use the rigrt databases by the command So if I want to use the latest updated database,I must download the new version of sourmash on github? |
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yes, that's the right database! The new database will not change your matches in this case. if you get a lot of 'nomatch' that should mean that most of your bins are unknown at the species/genus level. You can try using a k-mer size of 21, but your best bet is probably to switch to something that does tax classification at the protein level, such as CheckM. |
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I am so grateful that you replied to my message.Thank you very much! Best wishes to you . |
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thank YOU for touching base over this problem! I'm sure others are having it too. |
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(I will close this when we have dealt with the database issue :) |
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So I am having the same issue originally posted (assertion error). The software was installed with conda and can generate signatures but all of the commands to classify the signatures throws an assertion error. It doesn't seem to work for either database. Do I need to install a different version of sourmash? Thank you. |
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Hi Brian, apologies again. I should have waited to update the databases :)
Try the LCA databases here,
https://osf.io/zskb9
_or_ update from the latest github master to use the databases you've already
downloaded.
(In our (limited) defense we're getting ready for an actual 2.0 release and
wanted to avoid releasing 2.0.0a11.)
best,
--titus
On Fri, Jan 04, 2019 at 07:52:45AM -0800, Brian-No wrote:
So I am having the same issue originally posted (assertion error). The software was installed with conda and can generate signatures but all of the commands to classify the signatures throws an assertion error. It doesn't seem to work for either database. Do I need to install a different version of sourmash?
Thank you.
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Reply to this email directly or view it on GitHub:
#597 (comment)
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C. Titus Brown, ctbrown@ucdavis.edu
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I'll release 2.0.0a11 today, with the latest master. We did merge a bunch of PRs since a10...
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Thank you, the mark2 database worked. Looking forward to the update. |
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PR submitted to bioconda bioconda/bioconda-recipes#12919 |
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Thank you ! |
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thx @luizirber ! |
When I was running sourmash lca classify,I got this problem:
Traceback (most recent call last):ca.json.gz File "/home/lizongjun/miniconda3/bin/sourmash", line 11, in <module> sys.exit(main()) File "/home/lizongjun/miniconda3/lib/python2.7/site-packages/sourmash/__main__.py", line 77, in main cmd(sys.argv[2:]) File "/home/lizongjun/miniconda3/lib/python2.7/site-packages/sourmash/lca/__main__.py", line 54, in main cmd(sysv_args[1:]) File "/home/lizongjun/miniconda3/lib/python2.7/site-packages/sourmash/lca/command_summarize.py", line 99, in summarize_main dblist, ksize, scaled = lca_utils.load_databases(args.db, args.scaled) File "/home/lizongjun/miniconda3/lib/python2.7/site-packages/sourmash/lca/lca_utils.py", line 282, in load_databases lca_db.load(db_name) File "/home/lizongjun/miniconda3/lib/python2.7/site-packages/sourmash/lca/lca_utils.py", line 162, in load assert version == '1.0' AssertionErrorThis is my command:
sourmash lca summarize --db genbank-k51.lca.json.gz --query SB5.bin.9.orig.b.fa.sigCan you help me solve this problem?
Thank you very much!
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