java.lang.RuntimeException: Unable to parse clonotype string 4

[yueli8]

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```




[_vdjtools_error (3).log](https://github.com/mikessh/vdjtools/files/15221250/_vdjtools_error.3.log)
[36_clonotypes.TRA.txt](https://github.com/mikessh/vdjtools/files/15221254/36_clonotypes.TRA.txt)

[adhithyasimha]

You're trying to convert clonotype data from the MiXCR format to the vdjtools format, but you're encountering an error due to missing mandatory columns in the input file. To fix this, you can use the mixcr exportClones command to export the clonotypes to the vdjtools format, and then use the vdjtools Convert tool to convert the clonotypes to the VDJ format. Here are the steps:

1.Export the clonotypes to the vdjtools format using the mixcr exportClones command:

mixcr exportClones 36_clonotypes.TRA.vdjca --vdjtools-format TRA.txt

2.Convert the clonotypes to the VDJ format using the vdjtools Convert tool:

java -jar vdjtools-1.2.1.jar Convert -S MiXcr TRA.txt TRA_vdj.txt

[yueli8]

@adhithyasimha

Thank you so much for your quick response!

I used mixcr analyze command. It comes out 36.vdjca and 36.clna files. It doesn't come out 36_clonotypes.TRA.vdjca file.

Then I used exportClones command convert 36.clna to 36_clonotypes.TRA.tsv file.

Thank you in advance for your great help!

Best,

Yue

ThinkStation-P330:~/sph_data/mixcr_dev$ java -Xmx40g -jar mixcr.jar analyze 10x-sc-xcr-vdj --species hs 36_1_paired.fastq.gz 36_2_paired.fastq.gz 36

ThinkStation-P330:~/sph_data/mixcr_dev$ java -Xmx40g -jar mixcr.jar exportClones --chains TRA 36.clna 36_clonotypes.TRA.tsv

[yueli8]

@adhithyasimha

Thank you so much for your great help!

Best,

Yue

milaboratory/mixcr#1617

Open the 36_clonotypes.TRA.tsv file, then change the column name of readCount, readFraction to cloneCount, cloneFraction , and save. It is still *.tsv file.

ThinkStation-P330:~/sph_data/vdjtools-1.2.1$ java -jar vdjtools-1.2.1.jar Convert -S MiXcr 36_clonotypes.TRA.tsv 36_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 36_TRA.txt
[Tue May 07 16:36:44 CST 2024 Convert] Reading sample(s)
[Tue May 07 16:36:44 CST 2024 Convert] 1 sample(s) loaded
[Tue May 07 16:36:44 CST 2024 SampleStreamConnection] Loading sample 36_clonotypes.TRA
[Tue May 07 16:36:45 CST 2024 ClonotypeStreamParser] Finished parsing 10061 lines. 1 header and 0 bad line(s) were skipped. Bad line statistics: NO_CDR3NT=0, NO_CDR3AA=0, NO_V=0, NO_J=0, ZERO_COUNT=0, ZERO_FREQ=0, BAD_LINE=0
[Tue May 07 16:36:45 CST 2024 SampleStreamConnection] Loaded sample 36_clonotypes.TRA with 106 clonotypes and 760142 cells. Memory usage: 0 of 7 GB
[Tue May 07 16:36:45 CST 2024 Convert] Processed 1 sample(s).. Writing output
[Tue May 07 16:36:45 CST 2024 Convert] Finished

[adhithyasimha]

Happy to Help 👍