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emergency!!!! should i edit the immmetadata.txt file?or should i change the "every sample.tsv file "form "TRB folder “ which realized by using mixcr #3

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jialin-li-cell opened this issue Aug 11, 2024 · 0 comments

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@jialin-li-cell
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ljl@Jerry:~/vdjtools-1.2.1$ java --illegal-access=deny --add-opens java.base/java.lang=ALL-UNNAMED -jar vdjtools-1.2.1.jar Convert -S mixcr -m /home/ljl/TRB/TRB.immmetadata.txt VDJtools
Executing com.antigenomics.vdjtools.misc.Convert -S mixcr -m /home/ljl/TRB/TRB.immmetadata.txt VDJtools
[Sun Aug 11 14:31:50 CST 2024 Convert] Reading sample(s)
[Sun Aug 11 14:31:50 CST 2024 Convert] 16 sample(s) loaded
[Sun Aug 11 14:31:50 CST 2024 SampleStreamConnection] Loading sample 1
[ERROR] java.lang.RuntimeException: Unable to parse clonotype string 0 2391.0 4.2617487286495927E-4 TGTGCCAGCAGCTTAGCGGGCACAGATACGCAGTATTTT [[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[[ TRBV7-900(369.6) TRBJ2-300(477.8) 476|494|513|0|18||180.0 21|41|69|19|39||200.0 TGTGCCAGCAGCTTAGCGGGCACAGATACGCAGTATTTT 58 CASSLAGTDTQYF :::::::::0:1:18:::::19:-1:39::: for MiXcr input type: Some mandatory columns are absent in the input file., see _vdjtools_error.log for details

should i edit the immmetadata.txt file? or should i change the "every sample.tsv file "from "TRB folder “ which got by using mixcr "analyze method ", thanks!!!!

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