Closed irinatu closed 10 months ago
Psirving
commented
1 year ago I'm not entirely certain, but I think this means that SequenceCorrector is detecting multiple variants and that they are too different to merge into a single "correct" sequence. For example, if there were two alleles that are multiple SNPs away from the provided fasta in different directions, it might produce this error.
irinatu
commented
1 year ago Thank you for a prompt reply. Best regards, Irina.
From: Patrick Irving @.> Date: Thursday, 3 November 2022 at 17:15 To: Weeks-UNC/shapemapper2 @.> Cc: irinatu @.>, Author @.> Subject: Re: [Weeks-UNC/shapemapper2] problem with sequence corrector (Issue #37)
I'm not entirely certain, but I think this means that SequenceCorrector is detecting multiple variants and that they are too different to merge into a single "correct" sequence. For example, if there were two alleles that are multiple SNPs away from the provided fasta in different directions, it might produce this error.
— Reply to this email directly, view it on GitHubhttps://github.com/Weeks-UNC/shapemapper2/issues/37#issuecomment-1302346930, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADCWFTKRHVVSXYXV5CPA6UDWGPQJHANCNFSM6AAAAAARV7RFFI. You are receiving this because you authored the thread.Message ID: @.***>
I have Error message that I do not understand completely. Could you help me, please?
Running SequenceCorrector at 2022-11-03 11:25:43 . . .
ERROR: Component "SequenceCorrector" failed, giving the following error message:============================================================== Traceback (most recent call last): File "/home/irina/bin/shapemapper-2.1.5/internals/python/pyshapemap/../../bin/make_variant.py", line 430, in
merged_variants)
File "/home/irina/bin/shapemapper-2.1.5/internals/python/pyshapemap/../../bin/make_variant.py", line 325, in correct_sequence
raise RuntimeError(s)
RuntimeError: Error: Unable to determine variant sequence. Conflicting (overlapping) variant sequences present.