wtdbg2 not a PGZF format error

[weilu1998]

Hi,

Thanks for providing this useful tool! I was able to run the test sample successfully. I encountered many Errors when using my own sample VCF output from sniffles2. Many of them are in the wtpoa-cns step. Do I need to do some preprocessing for the sniffles2 output VCF file? Currently, I only removed the BND type SV that cause many problems for this pipeline.

-- Starting program: wtpoa-cns -t1 -d /scratch/refine_SV_breakpoint/breakpoint_refinement/contig_fasta131913529b69b0.fa -i - -fo /scratch/refine_SV_breakpoint/breakpoint_refinement/polished_fasta1319131b43f946.fa
-- pid                   1459766
 -- Error: not a PGZF format at 2 block, in thread_pgz_func -- pgzf.h:369 --

[malemay]

Hi Phragmites, Thank you for your interest in our software! I have developed this software using the first version of Sniffles; this might be why you get an error when using it with the output from Sniffles2. Would you mind sending me your VCF or part of it so I can reproduce the bug and try to fix it? I would also need the code that you use to launch the breakpoint refinement pipeline. Thank you, Marc-André

…

________________________________ From: Phragmites ***@***.***> Sent: February 2, 2023 12:22 PM To: malemay/breakpoint_refinement ***@***.***> Cc: Subscribed ***@***.***> Subject: [malemay/breakpoint_refinement] wtdbg2 not a PGZF format error (Issue #1) Hi, Thanks for providing this useful tool! I was able to run the test sample successfully. I encountered many Errors when using my own sample VCF output from sniffles2. Many of them are in the wtpoa-cns step. Do I need to do some preprocessing for the sniffles2 output VCF file? Currently, I only removed the BND type SV that cause many problems for this pipeline.

-- Starting program: wtpoa-cns -t1 -d /scratch/refine_SV_breakpoint/breakpoint_refinement/contig_fasta131913529b69b0.fa -i - -fo /scratch/refine_SV_breakpoint/breakpoint_refinement/polished_fasta1319131b43f946.fa -- pid 1459766 -- Error: not a PGZF format at 2 block, in thread_pgz_func -- pgzf.h:369 -- — Reply to this email directly, view it on GitHub<#1>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AESZYZOCOV7BYYL3II6BC3DWVPUMLANCNFSM6AAAAAAUPJRIM4>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[weilu1998]

Hi @malemay

Thanks for the quick reply! I just sent you a box link through email.

Thanks,
Wei