No JSON file output from absrel

[ShanfenO]

Dear @spond ,
When I run the command ：
"hyphy absrel --alignment TAS1R1.align.mafft.trimal.cds.afa.genome.filtered.species.fasta --tree tree.newick > TAS1R1.hyphy.log"
,only a log file is generated without any JSON file output. Could you tell me what might have gone wrong?Many appreciate you!

Sam

[spond]

Dear @ShanfenO,

Are there any error messages in the log file? If the analysis terminates prematurely, the JSON file may be empty.

Best,
Sergei

[ShanfenO]

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

[ShanfenO]

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

[spond]

Dear @ShanfenO,

1. 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?
2. 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

[ShanfenO]

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

[spond]

Dear @ShanfenO,

1. 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 try aBSREL outside the scheduler for a test run just to make sure that json files are being generated as expected.

2. 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

[ShanfenO]

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