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Published 20 hours ago • verified publisher icon mpieva

iterations issue

Open npsonis opened this issue 2 years ago • 4 comments

Hi I am using mia to estimate contamination levels. It works for all of my samples but one, for which I get this error:

Making kmer list for k-mer filtering... Starting to align sequences to the reference... ... Repeat and score filtering Repeat and score filtering Generating new assembly consensus Starting assembly iteration 2 Repeat and score filtering mia: line 15: 23680 Segmentation fault mia -r rCRS.fa -f ${SAMPLE}.fastq -c -C -U -i -F -k 14 -m ${SAMPLE}.fastq.maln

When I disable iterations (-i flag replaced by -n) it works. I also tried different k values but I do not think that it is related to the issue.

Any thoughts? Can I trust the results without the iterations?

npsonis avatar Jun 21 '22 09:06 npsonis

How big is the fastq file? I'm wondering if it's crashing because of memory issues.

aersoares81 avatar Jun 21 '22 13:06 aersoares81

Not so different compared to the rest... In fact, larger files worked without an issue...

npsonis avatar Jun 21 '22 13:06 npsonis

I have the same issue as you, this error occurred in some data. How do you solve this problem in the end? @npsonis

1993zsj123 avatar Feb 06 '23 14:02 1993zsj123

Hi, I did not... This was in a prescreening run so I did not invest my time to solve it. When I run the same sample (but deep sequencing) I did not meet the same issue.

Best

npsonis avatar Feb 06 '23 15:02 npsonis