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mskcc / tempo

CCS research pipeline to process WES and WGS TN pairs
https://cmotempo.netlify.com/
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Neoantigen Error: not one of the known HGVSc strings #838

Closed gongyixiao closed 3 years ago

gongyixiao commented 3 years ago

Failed 4 times, for the same reason.

In the current WES repo, I got this for two different tumors, but the same normal:

2c/ecc9df   RunNeoantigen   s_C_WNLXAP_P001_d__s_C_WNLXAP_N001_d    FAILED  1   1   20d 20h -   64 GB   4
e9/a1cb43   RunNeoantigen   s_C_WNLXAP_P002_d__s_C_WNLXAP_N001_d    FAILED  1   1   20d 20h -   64 GB   4
[gongy@terra v1.3.x]$ cat work/2c/ecc9df824239f62f42597c508c2690/.command.log work/e9/a1cb4311281bf387073de347b6716f/.command.log | grep HGVSc
Error: not one of the known HGVSc strings: c.-10_20dupTATTCGCAAGATGAAGAAGTTTTTCGACTC
Error: not one of the known HGVSc strings: c.-10_20dupTATTCGCAAGATGAAGAAGTTTTTCGACTC
anoronh4 commented 3 years ago

similar issue to this one: https://github.com/taylor-lab/neoantigen-dev/issues/7

anoronh4 commented 3 years ago

similar situation found for s_C_7CFK1U_P001_d__s_C_7CFK1U_N001_d

$ cat /juno/work/tempo/wes_repo/workspace/workDir/v1.3.x/work/c5/8067bc5fa9a01b8fa964e4d923a998/.command.log
Error: not one of the known HGVSc strings: c.-1_1dupAA