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cliu32 / Athlon

Accurate Typing of Human Leukocyte Antigen (HLA) by Oxford Nanopore Sequencing
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Blast - hitpolicy #6

Open jrob119 opened 6 years ago

jrob119 commented 6 years ago

I have blasr (taken from SmrtAnalysis 2.3) installed but get the following error;

"ERROR: hitPolicy is not a valid option."

This causes an error, trying to run this step.

cliu32 commented 6 years ago

Probably similar problem as #5. We are likely to create a virtual box for distribution in the future. For now, could you please try installing blasr directly from Linux, or checking out the legacy versions listed here: https://packages.ubuntu.com/xenial/blasr

jrob119 commented 6 years ago

Thanks, I have the version installed that matches the xenial blasr version. This appears to have the same SAM format problems and does not have the hit policy option.

adbeggs commented 6 years ago

Hi both

I have had exactly the same problems and have gone ahead and made the Xenial virtualbox image with all deps and it runs fine now.

There is an issue with the script in that there were a couple of things that needed changing for the specific version, like bedtools groupby for instance.

Happy to share if anyone's interest.

@jrob119 I assume you're doing the same as I am (HLA typing for transplant?) - perhaps we should talk off line?

A

cliu32 commented 6 years ago

@adbeggs Glad to hear you got the script running and thank you so much for sharing. My apology for the lack of prompt support for this tool, which may be a chronic issue. I was not able to locate any blasr 2.0.0 online myself or to verify the version of the Xenial blasr. Sounds like the Xenial blasr worked with your adjustment to the code. Thanks again.
@jrob119 Thanks for the follow-up question. Sorry for the delay. Hope Andrew's solution works for you as well.

mnk2017 commented 5 years ago

@adbeggs could you share your fix for the groupby lines in the script? I've been unable to get this script to work when it reaches ranking the 1 field coverage, the failure is in the groupby command, but I can't figure out why it's a problem. Thanks!

cliu32 commented 5 years ago

The groupby is a Linux command. Should install it in Linux if not in place already.

On Mar 17, 2019, at 12:09 PM, mnk2017 notifications@github.com wrote:

@adbeggs could you share your fix for the groupby lines in the script? I've been unable to get this script to work when it reaches ranking the 1 field coverage, the failure is in the groupby command, but I can't figure out why it's a problem. Thanks!

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mnk2017 commented 5 years ago

Thanks. Groupby is installed and line 47 and 50 call groupby and work fine in athalon.sh, generating the _2f_coverage.csv and _3f_coverage.csv. But line 53 which generates the *_1f_coverage.csv errors out in my hands on the groupby command. It must be something specific to my environment. I just was wondering if @adbeggs had some insight since he mentioned above that "there were a couple of things that needed changing for the specific version, like bedtools groupby for instance."