ERROR: No anonym seed reads found! #380
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I am trying to make an animal mitochondrial assembly using my own seed, but when I run using the -F anonym and -s and --genes options it still gives me the error that it was looking for "anonym" seeds and could not find them ("ERROR: No anonym seed reads found!"). When I run it with "-F animal_mt" I get "ERROR: No animal_mt seed reads found!" Can you help me? It looks like it is not using the seed I am providing. I am not sure what I am doing wrong. I am pasting the -F anonym example and output below (variables point to local file locations). Thanks, ~/biotools/bin/GetOrganelle/get_organelle_from_reads.py -1 $FORWARD -2 $REVERSE -R 10 -k 21,45,65,85,105 -F anonym -o $ANIMAL_MT_OUT -s $SEED --genes $SEEDLABELS ############## GetOrganelle v1.8.0.1 get_organelle_from_reads.py assembles organelle genomes from genome skimming data. Python 3.8.3 (default, May 19 2020, 18:47:26) [GCC 7.3.0] 2025-07-02 11:22:36,022 - INFO: Setting '--target-genome-size 0' for estimating the word size value for anonym type. 2025-07-02 11:22:36,896 - INFO: Pre-reading fastq ... 2025-07-02 12:08:38,561 - INFO: Making seed reads ... Total cost 4263.92 s ############################## |
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Replies: 2 comments 1 reply
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Hi Michael, thanks for reaching out here! As far as I can tell from the log and your detailed description, you've been using anonym and animal_mt successfully (in terms of executing the script) with your provided seed and label files. The ERROR "XXX seed reads found" means no reads hit the provided seed database. This happens largely due to 1) a lack of target reads or 2) too much sequence divergence between the database and the target sample. Thanks for trying 1.8.0.1 by the way. For using the full function, you also need to install gekko, which can be easily installed using |
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Thanks. To clarify, when it says "no anonym seed reads found" it means that it is properly recognizing the custom seed sequence and that no reads mapped to it? I was worried it was trying to find a file called "anonym," which does not exist. We are using a huge amount of reads and also using a full mitochondrial reference from another bivalve speceis within the same family. Is there any way to decrease the specificity required to allow mapping with animals like bivalves that have high mtDNA divergence rates? I am currently running it with a COI fragment that I know matches exactly but only covers a small fragment of the total mtDNA. |
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I can confirm that this was due to no matches of my sequence reads to the supplied reference, even though it was a mtDNA genome from a bivalve from the same family! Mito sequence divergence in bivalves is pretty high! Good news is that GetOrganelle was able to bootstrap what appears to be the entire mitogenome with just the COI sequence (less than 1kb), as long as I put in some reasonable length guidelines: This is super useful, since there are a lot of diverse animals where we have the COI sequence, but nothing else, so it is great that this program is able to extend from that. It is not annotated, but I can deal with that later. Thanks for your help in clarifying the error messages I was getting! And thanks for the tool! |
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Hi Michael, thanks for reaching out here! As far as I can tell from the log and your detailed description, you've been using anonym and animal_mt successfully (in terms of executing the script) with your provided seed and label files. The ERROR "XXX seed reads found" means no reads hit the provided seed database. This happens largely due to 1) a lack of target reads or 2) too much sequence divergence between the database and the target sample.
Thanks for trying 1.8.0.1 by the way. For using the full function, you also need to install gekko, which can be easily installed using
pip.