Error while running command buildLibrary java.lang.IllegalArgumentException: Unknown symbol " " about mixcr HOT 6 CLOSED

Hi, could it be that you have some extra space in your command that is not shown here. I have copy pasted your command and it works fine (I only changed the fasta files' names to the one I have).

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Hi, the problem was in the fasta files because I found some blank spaces there. Sorry for the inconvenience!

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Hi, one question related to this.
When I run the code above (build a library for TCR alfa), the fact that it does not find any alignment with any of the V segments in the fasta file is not normal, isn't it?
I tried --v-gene-feature VRegion and --v-gene-feature VExon2 and I get the same for every V segment:
For example:

Processing: aOncmyk_Chr8_CM023226.2_TRAV17-3_TRAV_130-35_F_61467747_61468085 (F) TRA
No alignments found.

I send you the command line in pdf and the library I got by executing this command...
Oncorhynchus_mykiss-TRA.json.gz
library_terminal.pdf

And when I run debugLibrary with the library (using --v-gene-feature VRegion):
mixcr debugLibrary Oncorhynchus_mykiss-TRA.json.gz
for each V segment, I get this at the beginning:

aOncmyk_Chr8_CM023226.2_TRAV17-3_TRAV_130-35_F_61467747_61468085 (F) TRA : 8022

WARNINGS: 
Unable to find CDR3 start
VRegion contains a stop codon

And with the library (using --v-gene-feature VExon2), I get this for each V segment:

aOncmyk_Chr8_CM023226.2_TRAV17-3_TRAV_130-35_F_61467747_61468085 (F) TRA : 8022

WARNINGS: 
Unable to find CDR3 start

Maybe I'm using the wrong commands... Could you help me please?
Thank you in advance!

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can you share the FASTA files for V genes?

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can you share the FASTA files for V genes?

docs.zip

Hi,
I modified the headers of the fasta files just in case, and I reran the code again and nothing, same problem again... And also for the TRB... I send you the V and J segments for TRA, a copy of the terminal when running the code and the library that I get as output... Please, help me!

Thank you in advance!

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Hi, so the main issue here is that sequences seem to have some extra nucleotides before the first FR1 position. Thats why FR1 is identified erroneously. You can either fix it in the FASTA, or use {CDR1Begin:VEnd} feature instead.
Oncorhynchus_mykiss-TRA.json

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