hla.p.json

[drkoryjohns]

Hello,

I am trying to run arcasHLA using the test commands provided on the git page but incur error:

traceback (most recent call last): File "/arcasHLA/scripts/genotype.py", line 707, in with open(hla_json, 'r') as file: FileNotFoundError: [Errno 2] No such file or directory: '/arcasHLA/scripts/../dat/ref/hla.p.json'

When I inspect the reference.py script, it appears there is this line that is commented out:

https://github.com/RabadanLab/arcasHLA/blob/master/scripts/reference.py#L458

Is that the issue, should this line be uncommented or how can I circumvent the error?

Thank you,

Kory Johnson

[YuJiandongBio]

Same problem, any solution?

[olekskrav]

Hi Kory. Thanks for the interest in our tool, and sorry for the delay in replying!

Unfortunately, we were not able to reproduce the error. Can you let us know which version of arcasHLA you have used, and what where specific commands leading to the error? We recommend using the latest version built with our official docker file as described here.

Also, just to provide some insight, the file hla.p.json should be generated during the reference step which is implicitly performed by the check_ref() function call in genotype.py (currently at line 700).

Another way to generate the missing file is to manually run the reference command first as follows:

arcasHLA reference -v

The reference command clones the IMGT/HLA database and performs the necessary indexing needed later for the genotyping. In particular, it should create the files hla.fasta, hla.idx and hla.p.json in the dat/ref folder. (The -v option allows to observe the progress of the command.)

Please let us know if you observe any issue with running the reference step and if all these files are successfully generated.

As for the commented line you mentioned, it should not be related to the issue. It was due to the update in which we switched from the pickle to json format in the intermediary files.

[drkoryjohns]

Thanks for getting back to me! The team that supports the HPC I use, NIH Biowulf, installed another instance and it worked no issue! Best, Kory

Kory R. Johnson, MS, PhD Bioinformatics Core Director, Information Technology Program (ITP), Division of Intramural Research (DIR), National Institute of Neurological Disorders & Stroke (NINDS), National Institutes of Health (NIH), Bethesda, Maryland

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From: Oleksandr Kravets @.> Sent: Thursday, October 13, 2022 5:15 PM To: RabadanLab/arcasHLA @.> Cc: Johnson, Kory (NIH/NINDS) [E] @.>; Author @.> Subject: [EXTERNAL] Re: [RabadanLab/arcasHLA] hla.p.json (Issue #92)

Hi Kory. Thanks for the interest in our tool, and sorry for the delay in replying!

Unfortunately, we were not able to reproduce the error. Can you let us know which specific commands did you run and if you used the latest version of arcasHLA?

Just to provide some insight, the file hla.p.json should be generated during the reference step which is implicitly performed by the check_ref() function call in genotype.py (currently at line 700https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FRabadanLab%2FarcasHLA%2Fblob%2Fmaster%2Fscripts%2Fgenotype.py%23L700&data=05%7C01%7Cjohnsonko%40ninds.nih.gov%7C9d5605e6b4cb454901c108daad5ff4bd%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638012924881241480%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=it0Vhlefet%2FE3eayJt7FG2MToxuJHm5dnTBshHDK4Is%3D&reserved=0).

Another way to generate the missing file is to manually run the reference command first as follows:

arcasHLA reference -v

The reference command clones the IMGT/HLA database and performs the necessary indexing needed later for the genotyping. In particular, it should create the files hla.fasta, hla.idx and hla.p.json in the dat/ref folder. (The -v option allows to observe the progress of the command.)

Please let us know if you observe any issue with running the reference step and if all these files are successfully generated.

Also, the commented line you mentioned should not be related to the issue. It was due to the update in which we switched from the pickle to json format in the intermediary files.

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[olekskrav]

Great, thanks for letting us know!