Welcome @pratibha! I suspect the problem here is that the minimum date is later than the maximum date, so no strains can pass the filters.
Can you try swapping these constraints on the dates (or correcting them) and see if that fixes the issue?
Thanx, but unfortunately it did not worked.
i would like to share my files. To see if I any format mistake in files.
Will you tell me the email id where i can share those.
Hello,
I have tried this option too but it is not working for me.
I would like to share my data files with you.
Please let me know further. as it is important for me in my analysis.
Thanks and Regards
Pratibha
Ah, I’m sorry that didn’t work, @pratibha! There must be another issue in addition to the min/max date swapping.
Before sharing files, could you share the contents of the filter log file (logs/filtered.txt) here? This output should list the counts of all the strains that were filtered along with the reasons why they were filtered. We might be able to diagnose the problem from this output alone.
Hello, I have created new files using which i run nextstrain.
the content of the filter log file is:
WARNING: A sequence index was not provided, so we are generating one. Generate your own index ahead of time with augur index and pass it with augur filter --sequence-index.
3 strains were dropped during filtering
1 had no sequence data
1 had no metadata
1 of these were dropped because they were in [‘defaults/exclude.txt’, ‘results/to-exclude_test-data.txt’]
0 of these were dropped because of ‘division=USA’
0 of these were dropped because they were shorter than minimum length of 27000bp
0 of these were dropped because of their date (or lack of date)
0 strains were added back because they were requested by include files
3 strains from include files were not added because they lacked sequence or metadata
3 strains passed all filters
but ahead it is giving error
Hi @pratibha – we recently added some functionality which relies on the epiweeks package being installed - the error you are seeing is because this package is missing from your system. To install it, please see the instructions for the v8 release as the exact command to use varies with how you’ve setup your system (instructions courtesy of @jlhudd).
1 Like
Thanks… I have solved The problem…
I got the output too.
Hi! I see the same error using Broadinstitute’s sarscov2_nextstrain workflow in Terra.bio. Any idea if this workflow would be updated anytime soon to include the missing package?
Hello, I’m having a very similar issue in which all strains are dropped:
ERROR: All samples have been dropped! Check filter rules and metadata file format.
19172 strains were dropped during filtering
9586 had no metadata
9586 of these were dropped by --exclude-all
20 strains were added back because they were in results/similarity/sample-focal.txt
I tried looking for inconsistencies in the metadata as suggested in this thread and created and checked the sequence index. Everything looks good so any help getting rid of this error would be greatly appreciated!