Unable to load fermi-lite native library /libbwa.Linux.so

[santoshatanur]

Hi

I have installed gridss via conda. I am getting the following error when I run gridss. Could you let me know how to fix it.

WARNING 2021-12-12 09:48:35 BwaAligner Found bwa index files. Attempting to create image from bwa index files
ERROR 2021-12-12 09:48:36 PrepareReference
java.lang.IllegalStateException: Misconfiguration: Unable to load fermi-lite native library /libbwa.Linux.so
at org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.loadNativeLibrary(BwaMemIndex.java:470)
at org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.createIndexImageFromIndexFiles(BwaMemIndex.java:121)
at au.edu.wehi.idsv.alignment.BwaAligner.createBwaIndexFor(BwaAligner.java:69)
at gridss.PrepareReference.doWork(PrepareReference.java:61)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at gridss.PrepareReference.main(PrepareReference.java:89)
Caused by: java.io.IOException: No such file or directory
at java.base/java.io.UnixFileSystem.createFileExclusively(Native Method)
at java.base/java.io.File.createTempFile(File.java:2090)
at java.base/java.io.File.createTempFile(File.java:2136)
at org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.loadNativeLibrary(BwaMemIndex.java:464)
... 5 more

[d-cameron]

What OS/CPU are you using?

[santoshatanur]

Linux HPC cluster with multiple nodes. Each node with 12 processor and 96gb memory.

…

________________________________ From: Daniel Cameron ***@***.***> Sent: 13 December 2021 00:44 To: PapenfussLab/gridss ***@***.***> Cc: Atanur, Santosh ***@***.***>; Author ***@***.***> Subject: Re: [PapenfussLab/gridss] Unable to load fermi-lite native library /libbwa.Linux.so (Issue #553) This email from ***@***.*** originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. What OS/CPU are you using? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#553 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AR4O47FLEPGLLM5WLNT7RE3UQU6YNANCNFSM5J4FOF5Q>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[d-cameron]

do you have write access to your java.io.tmpdir location?

Edit: on linux, this is typically /tmp

[santoshatanur]

No

…

________________________________ From: Daniel Cameron ***@***.***> Sent: 17 December 2021 02:00 To: PapenfussLab/gridss ***@***.***> Cc: Atanur, Santosh ***@***.***>; Author ***@***.***> Subject: Re: [PapenfussLab/gridss] Unable to load fermi-lite native library /libbwa.Linux.so (Issue #553) This email from ***@***.*** originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. do you have write access to your java.io.tmpdir location? — Reply to this email directly, view it on GitHub<#553 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AR4O47A4BQHIUBRGGTHVLODURKKSHANCNFSM5J4FOF5Q>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[d-cameron]

That'll be the issue. Set you temporary file location environment variable to a writable location.

…

On Fri, 17 Dec 2021, 18:35 Santosh Atanur, ***@***.***> wrote: No ________________________________ From: Daniel Cameron ***@***.***> Sent: 17 December 2021 02:00 To: PapenfussLab/gridss ***@***.***> Cc: Atanur, Santosh ***@***.***>; Author ***@***.***> Subject: Re: [PapenfussLab/gridss] Unable to load fermi-lite native library /libbwa.Linux.so (Issue #553) This email from ***@***.*** originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list< https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. do you have write access to your java.io.tmpdir location? — Reply to this email directly, view it on GitHub< #553 (comment)>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AR4O47A4BQHIUBRGGTHVLODURKKSHANCNFSM5J4FOF5Q >. Triage notifications on the go with GitHub Mobile for iOS< https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android< https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub >. You are receiving this because you authored the thread.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub <#553 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABOBYOEZLPGWZQ2OVUT7SRDURLR5VANCNFSM5J4FOF5Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you modified the open/close state.Message ID: ***@***.***>