Illumina/DRAGMAP

Segmentation fault. --build-hash-table

sukhanovaxenia opened this issue · 3 comments

sukhanovaxenia commented

To whom it may concer.

Recently tried to build hash table for human genome fasta of 14th chromosome, version hg38.

However after multiple tries and reinstallations each attempt continued ending up with the rror 'Segmentaton fault'.

I've also followed previous solution tips, mentioned in other issues (for instance, re-installation with make CFLAGS:=). Unfotunately, it didn't help.

Here is the code I launch from DRAGMAP dir:

dragen-os --build-hash-table true --ht-reference ~/hg38.chr14.fna --output-directory ~/ref

And the error I get:

`2022-02-09 04:12:51 [7feb2d8b7c00] Version: 1.2.1-7-gc87d93aa
2022-02-09 04:12:51 [7feb2d8b7c00] argc: 7 argv: dragen-os --build-hash-table true --ht-reference /home/yc-user/hg38.chr14.fna --output-directory /home/yc-user/ref

Building hash table from /home/yc-user/hg38.chr14.fna

Segmentation fault`

Look forward to hearing from you. Hope to recieve any suggestions and resolutions.

Your faithfully,

Sukhanova Xenia

rpetrovski commented
sukhanovaxenia commented

Xenia, can you please confirm that you did 'make clean ' before 'make CFLAGS:=' R.
…
On Wed, 9 Feb 2022, 04:23 sukhanovaxenia, @.> wrote: To whom it may concer. Recently tried to build hash table for human genome fasta of 14th chromosome, version hg38. However after multiple tries and reinstallations each attempt continued ending up with the rror 'Segmentaton fault'. I've also followed previous solution tips, mentioned in other issues (for instance, re-installation with make CFLAGS:=). Unfotunately, it didn't help. Here is the code I launch from DRAGMAP dir: dragen-os --build-hash-table true --ht-reference ~/hg38.chr14.fna --output-directory ~/ref And the error I get: 2022-02-09 04:12:51 [7feb2d8b7c00] Version: 1.2.1-7-gc87d93aa 2022-02-09 04:12:51 [7feb2d8b7c00] argc: 7 argv: dragen-os --build-hash-table true --ht-reference /home/yc-user/hg38.chr14.fna --output-directory /home/yc-user/ref Building hash table from /home/yc-user/hg38.chr14.fna Segmentation fault Look forward to hearing from you. Hope to recieve any suggestions and resolutions. Your faithfully, Sukhanova Xenia — Reply to this email directly, view it on GitHub <#26>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAXSY4MLRFDN3CHKT7SQXSLU2HT2HANCNFSM5N4LPTKQ . 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 are subscribed to this thread.Message ID: @.>

Dear R. Petrovski,

Sure, before assessing 'make CFLAFS:=' the command 'make clean' was perfomed.

rpetrovski commented

Can you please post you OS and gcc version details.

R.