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Unable to run the trio_longread.php pipeline #288
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If the samples are not contained in the NGSD database, you have to provide the processing system definition using the Here an example of system definition:
The
I hope that helps you |
Hello, this worked! Thank you!
and here is the log from it Another thing that I need clearance on is if I want to use the GRCH38_alt.fa instead of GRCH38.fa, where do I need to adjust the script? |
Did you analyze the samples individually with megSAP as well? Currently megSAP does not support alt-chromsomes. |
Hello,
I was able to install the megSAP pipeline and the NGSD database according to the instructions provided on GitHub and am now trying to run the trio_longread.php pipeline on our ONT data but couldn't get it to run. This is the command that I'm using:
php trio_longread.php -f /path/to/father.bam -m /path/to/mother.bam -c /path/to/child.bam -out_folder /home/labnigro/trio001 -steps vc,cn,sv,an,db -threads 20
but I get this error:
I tried to find a solution to this and it seems this has something to do with the NGSD database but I read that the NGSD database implementation is optional but I couldn't figure out how to NOT include it while running. I am stuck here and unable to go forward.
What might be the problem?
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