CalcBasicStats [ERROR] java.lang.RuntimeException: Unable to parse clonotype string 7 ...VDJtools input type: Unknown symbol "o"

[rosanababu]

Hi Mikessh,

Thanks for this wonder tool. I'm trying to do CalcBasicStats from TRUST4 output directly, I couldn't use "Convert" because there's no option "-S" for TRUST4. I'm getting following error, could you kindly advise how to process TRUST4 results to use your amazing tool...

[ERROR] java.lang.RuntimeException: Unable to parse clonotype string 9 6.716418e-02 TGTGCGAGAGGGCAGGACGGTGACTACGTGGGCGAGCCCGGGGAGTCTACTACTACTACTACATGGACGTCTGG out_of_frame IGHV1-301 IGHD1-2601 IGHJ6*04 . assemble1 0 for MiXcr input type: Some mandatory columns are absent in the input file., see _vdjtools_error.log for details

Many thanks, Rosana

[rosanababu]

Hi Mikessh,

This issue is solved by using: "grep -v out_of_frame TRUST4_report.tsv > TRUST_report_vdjformat.tsv". VDJtools downstream analysis with the filtered file is working fine now...

Please find below response from liulab-dfci/TRUST4.

TRUST4 uses "out_of_frame" in the amino acid field to represent the kind of non-productive CDR3. It seems VDJtools does not recognize this, and you can use "grep -v out_of_frame" to remove those lines.

Best wishes, Rosana