Assembly of animal mtgenome successful, but has a very low recruited ratio

[maikejetlin]

Hi everyone,

I am running a number of animal mtgenome assemblies (fish mtgenomes). Most of them came out successful on the first try, but I am currently trying to rerun the unsuccessful ones. I followed the advice I found on GetOrganelle's wiki page, and reran one of the unsuccessful assemblies with the output from its previous run as a seed. My code currently looks like this:

get_organelle_from_reads.py -1 reads_forward.fastq.gz -2 reads_reverse.fastq.gz -F animal_mt -o sample1_rerun -R 10 -t 16 -s sample1_firstrun/animal_mt.K115.contigs.graph1.1.path_sequence.fasta

I got a successful, circular assembly out of this, but after taking a closer look, I noticed that I got a very small amount of target organelle associated reads in the output. When I look at the log file from another assembly that did work on first try (without a seed), I see a recruited ratio of about 8.5% on the last round (round 10). When I look at the log file for the rerun with seed, I see a recruited ratio of only 0.019%. That part of the log file looks like this:

2025-04-15 12:25:48,518 - INFO: Round 5: 33876015/33876015 AI 6554 AW 262904
2025-04-15 12:25:48,520 - INFO: No more reads found and terminated ...

It says that no more reads were found after round 5, even though I specified 10 rounds, and the AI and AW look really low.

In comparison, the same part of the log file from one of the successful assemblies without seed looks like this:

2024-10-22 17:11:09,404 - INFO: Round 10: 45133200/45133200 AI 3859648 AW 66847642

I added the complete log file from the rerun below:

get_org.log.txt

The files containing the target organelle associated reads (extended_1_paired.fq, extended_2_paired.fq) in this output are only about 1.3MB, which is way smaller than those in the output of one of the other successful runs without a seed, which are all about 250MB or larger.

I was wondering if someone could help me interpret this, and let me know if these results are okay to work with? I did get a successful assembly with this run, but it just seems very strange to me, and I would like to be sure that my results are valid before I continue my analysis.

Thank you in advance!