TypeError: argument of type 'NoneType' is not iterable

1

I have download a fasts file from GISAID with the following format,

Spike|hCoV-19/Wuhan/WIV04/2019|2019-12-30|EPI_ISL_402124|Original|hCoV-19^^Hubei|Human|Wuhan Jinyintan Hospital|Wuhan Institute of Virology|Shi|China
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGA…

Then, I parse this file using augur command and get the following error message,

[(nextstrain) Lucys-MacBook-Pro:GISAID download 2021Jan6 lucy$ augur parse -s spikeprot0105.fasta
Traceback (most recent call last):
File “/opt/anaconda3/envs/nextstrain/bin/augur”, line 8, in
sys.exit(main())
File “/opt/anaconda3/envs/nextstrain/lib/python3.6/site-packages/augur/main.py”, line 10, in main
return augur.run( argv[1:] )
File “/opt/anaconda3/envs/nextstrain/lib/python3.6/site-packages/augur/init.py”, line 74, in run
return args.command.run(args)
File “/opt/anaconda3/envs/nextstrain/lib/python3.6/site-packages/augur/parse.py”, line 93, in run
if ‘name’ in args.fields:
TypeError: argument of type ‘NoneType’ is not iterable

Any comments are greatly appreciated.

2

So, what is the correct format of the .fasta file which is fed into the command “augur -sequences myFile.fasta” ?

3

Ah, augur parse requires specifying the --fields option to tell it how your FASTA sequence descriptions are formatted.

More details and examples are in the documentation for augur parse.