vdjtools

Question

[yueli7]

Hello,

I tried to use vdjtools comvert clonotypes to vdj format.

It said: "[ERROR] java.lang.RuntimeException: Unable to parse clonotype string 4".

Thanks in advance for great help!

Best,

Yue

ThinkStation-P330:~/sph_data/vdjtools-1.2.1$ java -jar vdjtools-1.2.1.jar Convert -S MiXcr 
36_clonotypes.TRA.tsv TRA.txt
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.codehaus.groovy.vmplugin.v7.Java7$1 
(file:/home/yueli/sph_data/vdjtools-1.2.1/vdjtools-1.2.1.jar) to constructor 
java.lang.invoke.MethodHandles$Lookup(java.lang.Class,int)
WARNING: Please consider reporting this to the maintainers of 
org.codehaus.groovy.vmplugin.v7.Java7$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective 
access operations
WARNING: All illegal access operations will be denied in a future release
Executing com.antigenomics.vdjtools.misc.Convert -S MiXcr 36_clonotypes.TRA.tsv 
TRA.txt
[Mon May 06 21:01:58 CST 2024 Convert] Reading sample(s)
[Mon May 06 21:01:58 CST 2024 Convert] 1 sample(s) loaded
[Mon May 06 21:01:58 CST 2024 SampleStreamConnection] Loading sample 
36_clonotypes.TRA
[ERROR] java.lang.RuntimeException: Unable to parse clonotype string 4   
not_calculated  ACCAGTATCAACCATG    no_quality_for_tag  1099.0   
0.0014457824985331688   179 6.020084886560076E-4     
TGCCTCGTGGGTGACATGGACCAGGCAGGAACTGCTCTGATCTTT    
[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[   TRAV4*00(1096.4)        TRAJ15*00(209.8)     
TRAC*00(195.6)  332|350|368|0|18||180.0     23|49|80|19|45||260.0       TGCCTCGTGGGTGACATGGACCAGGCAGGAACTGCTCTGATCTTT   58  CLVGDMDQAGTALIF :::::::::0:2:18:::::19:-3:45::: TRA for MiXcr input type: Some mandatory columns are absent in the input file., see _vdjtools_error.log for details

[Yan]

Oh, I got the same problem.

Yue, have you solved it?

[GenoMax]

If you have an identical issue then take a look inside _vdjtools_error.log file as suggested above.