CreateGermlines.py fails with error 'Germline sequence differs in length from input sequence by X characters.'

[Elinor Wing]

Hello,

I was having some problems running buildPhylipLineage as the germline and input sequences were occasionally different lengths. I saw that running CreateGermlines.py may help but I am getting a similar error back, that the germline sequence is a different length to the input sequence.

This is the code I am running:

CreateGermlines.py --format airr -d copybcr_and_seurat1_clone-pass.tsv -g dmask --cloned -r /Users/elinorwing/share/germlines/imgt/human/vdj/imgt_human_IGHV.fasta /Users/elinorwing/share/germlines/imgt/human/vdj/imgt_human_IGHD.fasta /Users/elinorwing/share/germlines/imgt/human/vdj/imgt_human_IGHJ.fasta --log log.txt

The input into this is what I got from DefineClones.py which seemed to work.

Am I missing a step?

Thanks!

[ssnn]

Hi Elinor. Sorry for the delay. Somehow I missed this issue. The CreateGermlines.py command seems correct. Maybe the issue was with the buildPhylipLineage settings. Notice it takes one clone as input, not the full db. I am closing this issue because it is old (sorry!) and I suspect you have figured a solution yourself. Please, reopen if needed.

[Kelly Dew-Budd]

I have also run into this problem. It works on the same data when --cloned is removed.

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Edit: I am using CreateGermline.py with scoper output reduced to only the relevant clonal family

[ssnn]

Are there NAs in the clone_id column? Kelly, can you please send us to [e-mail] example data to reproduce and debug the error?