HLA Typing Issue

[ElizabethBorden]

Hi,

I am running into an issue with the HLA typing that I cannot figure out. The program fails with the message: Traceback (most recent call last): File "bin/optitype_ext.py", line 31, in with open(input_optitype_result) as f: IOError: [Errno 2] No such file or directory: '/root/data/hlatyping/2021_01_08_05_28_37/2021_01_08_05_28_37_result.tsv' hla type process done.

And when I look at the log file for the hla typing it says: /root/source/seqan-seqan-v2.4.0/include/seqan/basic/basic_exception.h:363 FAILED! (Uncaught exception of type std::bad_alloc: std::bad_alloc)

From my research it looks like it is possibly a memory problem but I have expanded the volume I am working on twice with no change in the error. Do you have any estimates of how much space running the entire docker image requires?

Thank you! -Elizabeth

[ChiZhou-SITI]

Hi, ElizabethBorden,

Sorry for the delay. The HLA typing procedure in the pTuneos is performed by Optitype, which uses razers3 for reads mapping and extracting. As razers3 puts all mapped reads into memory, it requires large memory(>200G) if the sequencing depth of your data is deep (maybe >200X).

This issue could be handle by calling the HLA type using other tools such as POLYSOLVELR, xHLA, SOAP-HLA, hla-genotyper, HLA-HD, Kourima and, HLA-VBSeq by yourself. When you get the four-digital HLA type of your sample, you can provide it in the configure file field "hla_str". Then pTuneos would omit this procedure when running the whole pipeline.

Hope it helps!

Best, Chi

[ElizabethBorden]

That is very helpful! Thank you for your reply and I will try that!