Comments (8)
Dear @spond ,
Thank you very much for your help. I'm going to try switching servers and using other ways to see if that can solve these problems. As I am a beginner in bioinformatics, I might have many questions, so I really appreciate your enthusiasm.
Best,
Sam
from hyphy.
Dear @ShanfenO,
Are there any error messages in the log file? If the analysis terminates prematurely, the JSON
file may be empty.
Best,
Sergei
from hyphy.
Dear @spond,
TAS1R1.hyphy.out.txt
This is one of my log files.I dont see error messages expect "duplicate sequences".But there no JSON file make.
Best,
Sam
from hyphy.
Dear @spond ,
I have encountered another issue that I hope you can help me with. When running another gene, I received the following message:
code => Universal
*** PROBLEM WITH SEQUENCE ' Alaudala_cheleensis' (50 nt long, stop codons shown in capital letters)
atgccatcctttgct---ctcctttgt------------cta---tcaAT
Error:
The input alignment must have the number of sites that is divisible by 3 and must not contain stop codons in call to assert(absrel.codon_filter.sites*3==absrel.codon_data.sites, error_msg);
However, when I use the same sequence to run RAxML, the output appears normal. Could you provide some insight into what might be causing this discrepancy?
Best,
Sam
from hyphy.
Dear @ShanfenO,
- For the
aBSREL
run the log file indicates that the analysis did run to completion. Is the file at /slurm/home/zju/zhanglab/shenxulan/01.project/hyphy_work/00.data/TAS1R1/TAS1R1.align.mafft.trimal.cds.afa.genome.filtered.species.fasta.aBSREL.json` empty? - For the
50nt
file, if the alignment is not coding and in-frame, then you will see such an error.RAxML
usually takes in nucleotide data, so it won't care if the sequences are not in frame.
Best,
Sergei
from hyphy.
Dear @spond ,
1.There are no JSON files generated at all, so I am confused.
2.Do you have any better suggestions for modifications?
Thanks.
Best,
Sam
from hyphy.
Dear @ShanfenO,
-
I am not sure what is going on, because it could be system specific. Perhaps the process can't write to the directory. If you are running
hyphy
via schedulers, this could often be the case. It's also possible that the file is being written somewhere else if you spacified the--output
option on the command line. I would tryaBSREL
outside the scheduler for a test run just to make sure thatjson
files are being generated as expected. -
I can't really give you meaninful advice on data clean-up and alignment generation without knowing a lot more about how you are obtaining, trimming, and aligning your sequences. For this specific example, you could simply trim off the last two nucleotides from each sequence. As a word of caution, something as short as 50 nucleotides will be tricky to build trees for and may have other statisitcal issues. A 16-17 amino-acid long protein is probably an incomplete fragment of something larger.
Best,
Sergei
from hyphy.
Stale issue message
from hyphy.
Related Issues (20)
- Datamonkey does not recognized some sequences HOT 3
- Skipped user prompt in SM-2019.bf HOT 2
- Standard Error aBSREL HOT 4
- Questions about BUSTED and an error code 102 HOT 7
- FEL not working - Error included HOT 1
- Fix code scanning alert - Wrong type of arguments to formatting function
- hyphy MolecularClockF81.bf failed to compute a valid transition matrix HOT 2
- Multiple Testing Correction in BUSTED vs absREL HOT 5
- When does RELAX collapse rate classes? HOT 4
- Error: Internal error Constrained optimization failed, since a starting point within the domain specified for the variables couldn't be found. Set it by hand, or check your constraints for compatibility. HOT 3
- BUSTED error: tree_id_0 is not a supported object type in call to SetParameter HOT 9
- What is HyPhy calling the 2 nodes pointed at with arrows in this tree (image and txt file attached)? HOT 2
- aBSREL run time HOT 5
- Persistent error when running Gard HOT 5
- How to select positive signals of the foreground branch from the results of aBSREL modle HOT 4
- error HOT 7
- Analysis ends but does not progress to report generation HOT 5
- Failed to dereference error with FitMG94 and the local option HOT 2
- test for detecting compartmentalization in dataMonkey HOT 2
- DataMonkey not recognizing forground branches HOT 2
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