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rvalieris / LCS

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Error in rule split_fasta_lineages #12

Closed vinayrajput0005 closed 1 year ago

vinayrajput0005 commented 1 year ago

error.log Getting error while split_fasta_lineages. Script is not able to separate the linage data from GISAID full data.

Traceback (most recent call last): File "/data/Student_Data/Vinay/LCS-master/scripts/split_fasta_by_lineages2.py", line 52, in fn,lineage = l.rstrip().split(",") ValueError: not enough values to unpack (expected 2, got 1)

vinayrajput0005 commented 1 year ago

Pango lineage file is correct Lineages.csv (https://github.com/cov-lineages/pango-designation/blob/master/lineages.csv)

rvalieris commented 1 year ago

hello, this error implies the file have a line without any commas, can you run this command on the file and report back the results ?

grep -v , data/pango_designation/lineages.csv -m10
vinayrajput0005 commented 1 year ago

Error1.txt

Pls look on the error.

vinayrajput0005 commented 1 year ago

I removed PANGO_DESIGNATIONS_VERSION='v1.16' from shell command of script. Now it is downloading the latest lineages.csv file from the git repository. v.1.16 have some issue with the lineage file