Closed scorreard closed 1 year ago
Hi Solenne,
It seems to be an issue with your FASTA seq-ids/headers. I made a testing FASTA with the exact headers you included above and got a similar error. When I deleted the trailing None-None
from both sequences, it worked. When I deleted one None-None
, it also worked. When I replaced None-None
with two identical strings following the contigid:coordinates, I got the error.
We may need to post some guidelines about FASTA header formatting if we see more similar issues. If you want to move forward now I would just adjust the headers to make them simpler yet distinct.
Eric
Thanks Eric, I'll try removing the 'None-None' and will update you later this week!
Describe the bug seqtransform permanentFail
Hi team! Thanks for the tool, I used your tool several times after generating hifiasm assemblies and it worked perfectly, so not an installation issue. This time, I generated an assembly using Flye with both Hifi reads and ONT reads (simplex). I run fcs adaptor before scaffolding. I think the error is due to 2 contigs having the same length, even though they have different sequences. Looking forward your feedback,
Solenne
To Reproduce
I could share the genome with you if needed, but not sure it is necessary
Software versions :
Log Files
Tail of output/fcs_adaptor.log
Tail of output/debug.4dgcxzo_/tmp-outdirqnyhvbc2/seqtransform.log
grep '0-45901' -A 1 input_ont_fastq_1_assembly_consensus.cut250.tigmint.fa.k32.w100.z100.ntLink.scaffolds_cleaned3.fa ==> shows that the 2 sequences are different
Additional context I think it thinks the sequence is duplicated because it has the same coordinates '0-45901' even though they are different contigs?