iterations issue

[npsonis]

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?

[aersoares81]

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

[npsonis]

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

[1993zsj123]

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

[npsonis]

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