Comments (3)
We also ran into this issue and dug into a bit. It's caused by the extra POS_AA
column at the end.
Temporary solution for anyone having this issue
If you don't need the POS_AA data column, pre-process your variant files to remove this column.
In-depth Info
-
call_variants_from_plup
prints out aPOS_AA
(from a hardcoded set of column headings inside the function).
Lines 58 to 61 in 08aac33
-
common_variants
callsread_variant_file
which first checks if the headers are correct:
ivar/src/get_common_variants.cpp
Lines 25 to 30 in 08aac33
However this checks has 2 issues with it:
- It uses a parallel, and out of date, set of header names; it's missing
POS_AA
. This andcall_variants_from_plup
should be working with a single set of fields so there aren't two parallel structures to update when a change happens. - This code is has an out of bounds error, which is what's happening now. The loop will keep reading heading columns and index into
fields
even afterctr >= NUM_FIELDS
. The loop should terminate if there are more thanNUM_FIELDS
entries.
ivar/src/get_common_variants.cpp
Lines 3 to 8 in 08aac33
Also worth considering is changing the error message from common_variants
. It currently gives the incorrect impression that the header formats of A_variant and B_variant do not match each other, but what it actually means is that they don't match the expected header. Would be worth changing that message and also printing both the received header and the expected header.
from ivar.
Hi! Sorry that you're having issues, thanks for reaching out. Could you be more specific about the origin of "Part 4" and maybe share the .tsv files with me? Based on the given error, I would assume that the SNV variants files being used are not properly formatted but it's hard to tell without sample files!
from ivar.
Sure here is the link to .tsv files i got after process 3 in folder 6.Singlet-SNVs
Please let me know if you need any further information.
https://usaskca1-my.sharepoint.com/:f:/g/personal/zdk427_usask_ca/EolxZ7UcEDpPo6qFVXKB_KoBajXB_8WyJ6k5Kx3QoU3OjA?e=Y1ihRt
from ivar.
Related Issues (20)
- ivar version command not updated accordingly
- Clarification of new ivar consensus -c (minimum insertion frequency) parameter
- slow performance of ivar 1.3.2 HOT 1
- ivar trim -f option incompatible with new piping functionality HOT 3
- ivar trim hangs when using -f parameter
- Further speedup in iVar Trim primer finding HOT 3
- clarification of ivar trim -e option HOT 1
- iVar variants weird output HOT 5
- Error building the docker image from the Dockerfile HOT 3
- Discrepancy between samtools depth and TOTAL_DEPTH in ivar HOT 1
- Segmentation fault (core dumped) HOT 5
- Header format error in ivar filtervariants HOT 1
- REF_AA not consistent with actual AA at the position from reference protein fasta file HOT 2
- Variants returns multiple AA with 1.00 frequency HOT 2
- Parsing GFF_FEATURE
- iVAR inappropriately shifts position of reverse mapped reads for ONT data HOT 13
- Does ivar trim only from the ends of aligned BAM files? HOT 2
- weird variant TSV output HOT 1
- Incorrect amino acid numbering HOT 7
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