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Illumina / SMNCopyNumberCaller

A copy number caller for SMN1 and SMN2 to enable SMA diagnosis and carrier screening with WGS
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Error message when using cram file as input #3

Closed melnel000 closed 4 years ago

melnel000 commented 4 years ago

Hi

I am trying to run this program on a cram file and I am getting the following error message:

INFO:root:Processing sample FD01113665 at 2020-03-03 10:59:00.754390 [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/a811b3dc9fe66af729dc0dddf7fa4f13": Protocol not supported [E::cram_get_ref] Failed to populate reference for id 4 [E::cram_decode_slice] Unable to fetch reference #4 70044367..70079695 [E::cram_next_slice] Failure to decode slice

Please could you let me know what the problem might be.

Thanks!

xiao-chen-xc commented 4 years ago

Hi @melnel000, for a cram input, could you specify the reference fasta file with the --reference command so that the program can access the reference? Let me know if this does not solve the problem.

Thanks, Xiao

melnel000 commented 4 years ago

Thanks Xiao. I am able to run the program now.

Kind regards, Melissa

Dr Melissa Nel (MBChB, PhD) Neurology Research Group Division of Neurology, E8-30, Groote Schuur Hospital Department of Medicine, Faculty of Health Sciences University of Cape Town Observatory Cape Town 7925 Tel: +27836438393 email: melnel000@gmail.com

On Tue, Mar 3, 2020 at 6:20 PM Xiao Chen notifications@github.com wrote:

Hi @melnel000 https://github.com/melnel000, for a cram input, could you specify the reference fasta file with the --reference command so that the program can access the reference? Let me know if this does not solve the problem.

Thanks, Xiao

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