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wtsi-hpag / Scaff10X

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
MIT License
20 stars 3 forks source link

File Handling and Core Dumps. #6

Open harish0201 opened 5 years ago

harish0201 commented 5 years ago

Would it be possible to use named pipes in the very first step, i.e scaff_names series? Also, where would I be changing the default initial data copy behavior in the source code? Asking this as I'm currently working on a 1gb genome and we have a lane of data, so this would be likely eating up around 500Gb for just copying and extracting data.

Cursory checks with mkfifo as well as /dev/stdin for gunzipping and providing the same to scaff_names works well!

Can you share the Memory requirements as well, the only error seems to be "Core Dump, segmentation fault" on the terminal and quitting? Scaff10X seems to be giving up on another genome of about 400Mb with 100x coverage as well.

I'll share the log, currently I'm recompiling on another server.

harish0201 commented 5 years ago

Please find the Strace of the Core-dumps above. strace.log