align_trim ValueError: min() arg is an empty sequence (artic 1.2.1)

[thierryjanssens]

Hi all,

I am using artic for amplicon sequencing (nanopore) of viral genomes.
However, I get a consensus of N's and I traced back the problem to the align_trim step, since I get the following error:

ValueError: min() arg is an empty sequence

my virus.scheme.bed is:
virus 8 32 F1_On_LEFT 1 + CAACATATACCAACAACAAA
virus 2090 2112 R1_On_RIGHT 1 - ATGTGGAATTGCTCTAATGACT
virus 1878 1898 F2_ON_LEFT 1 + CGGACTGACTCTTACATTCG
virus 3954 3975 R2_On_RIGHT 1 - ATATGCCTGTACTGATCAACG
virus 3649 3674 F3_On_LEFT 1 + ACTGATTCCAATGGTACGAA
virus 5043 5057 R3_On_RIGHT 1 - GTAAATTGACTTCGGACAAAGAT
virus 4801 4820 F4_On_LEFT 1 + GCTGTGAGTGAGGTCCATA
virus 6313 6334 R4_On_RIGHT 1 - CTACGGATGTGTATGAACCAT

How can I get around this error?

Looking forward for any suggestions.

kind regards,

Thierry

[thierryjanssens]

Match with name of reference is primer name is essential.
referencename_primernumber_orientation
e.g. virus_1_LEFT
Solved.