Hi. I have been using LEfSe in the past and was successfully able to run the full pipeline with the Galaxy LEfSe tool. Now when I am trying to run the pipeline using new tabular files (I believe to be formatted correctly) and even old ones that successfully worked in the past I run into two errors:
Step A) Info
ERROR:galaxy.datatypes.data:Unable to count lines in file /export/galaxy-central/database/files/004/dataset_4265.dat
Step B) Error message:
Number of significantly discriminative features: 36 ( 36 ) before internal wilcoxon
Traceback (most recent call last):
File “/galaxy_venv/bin/lefse_run.py”, line 33, in
sys.exit(load_entry_point(‘lefse==1.1.2’, ‘console_scripts’, 'lefse_ru
I have tried to resolve these problems many different ways, but find myself very stuck. If anyone has any reconditions. It is greatly appreciated.
Apologies that you are running into issues. This week was the yearly maintenance on our servers and it has affected our Galaxy site, we are working on resolving this issue ASAP. Our software folks will let you know when we have fixed this bug.
Alternatively, you can use MaAsLin 2, a newer tool of ours, to do a similar analysis to LEfSe if you need to run something quickly.
Hello, I use galaxy online version found updated, the old version of the historical data is missing, when I want to re-analyze, in the ’ format data ’ step is always wrong :
ERROR : galaxy.datatypes.data : Unable to count lines in file / export / galaxy-central / database / files / 017 / dataset _ 17651.dat,
could you tell me what the reason is ?
I have the same problem in Galaxy, when will you could fix this bug?
"Traceback (most recent call last):
File “/galaxy_venv/bin/lefse_format_input.py”, line 33, in
sys.exit(load_entry_point(‘lefse==1.1.2’, ‘console_scripts’, ‘lefse_format_input.py’)())
File “/galaxy_venv/lib/python3.7/site-packages/lefse/lefse_format_input.py”, line 443, in format_input
feats = numerical_values(feats,params[‘norm_v’])
File “/galaxy_venv/lib/python3.7/site-packages/lefse/lefse_format_input.py”, line 192, in numerical_values
feats[k] = [float(val) for val in v]
File “/galaxy_venv/lib/python3.7/site-packages/lefse/lefse_format_input.py”, line 192, in
feats[k] = [float(val) for val in v]
ValueError: could not convert string to float: ‘ear’ "
Just wondering if there’s a timeline for when LEfSe will be up and running again? I’m trying to use MaAsLin 2 instead but I’m also getting errors when I import my tables… I see a new maintenance notice so I’m assuming it’s due to this?
Hello @wc1 ,
It looks like there are some formatting errors in your input file. Can you upload the lefse input file in the thread here and we can test it out and let you know.
To follow-up on my previous question. I still get the error: ERROR:galaxy.datatypes.data:Unable to count lines in file /export/galaxy-central/database/files/004/dataset_4265.dat
But I am able to complete all the steps in the workflow even with this error.
I am curious if this can just be ignored then?
Thank you for providing the file. I could replicate the error on my end as well. The format_data_for_lefse step1 is generating binary file for which galaxy is unable to count the files for. However, this will not interfere with the other steps for lefse visualizations. Please let me know if this is not the case.
Hi @garretta ,
Yes, confirmed that the error message can be ignored for now since all the steps are working fine. We will work on fixing the Unable to count lines in file error asap.
Please let us know if any other issues.
