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Error when running puma via docker #2
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sorry about the delayed response, would you mind sharing the fasta file? |
@yjx1217 I was able to reproduce the error via docker and was able to resolve it as follows:
This docker code runs successfully: Hopefully that works for you! |
Dear @RobJackson28, Thanks for the feedback and detailed information. I made the change according to your suggestions and the previous error disappeared. So many thanks for the tips! However, I now encountered a new error. Could you provide further help please? The error message is as follows:
The input fasta file is further attached. Best, |
@yjx1217, could you share the fasta sequence? |
Hi @KVDlab , The input fasta file has been attached in my last reply on the github issue page (#2). The direct URL is as follows: https://github.com/KVD-lab/puma/files/10516081/hom_sap_BF288.final.tidy.fa.gz :-) Best, |
This new 'puma.py' should run your sequence. That was a weird bug, thanks for pointing it out. |
Dear @KVDlab , Many thanks for the quick fix! I installed puma via docker. So is it possible to directly replace the old puma.py script with the new one within docker? If so, could you guide me how to do it? Thanks in advance! Best, |
@yjx1217 docker should be updated and good to go |
Dear @KVDlab , Many thanks for the fix and version update! The docker version 1.2.2 works nicely now! Best, |
Dear @KVDlab Sorry. While testing with HPV16 and HPV18 reference genomes, we noticed that although the annotated CDS/protein sequences seems to be correct, the genomic coordinates might be wrong. For example, in the reference annotation of HPV16 (https://www.ncbi.nlm.nih.gov/nuccore/NC_001526.4), the annotation shows>>
However, the annotation from PUMA suggests:
Best, |
Hi Jia-Xing,
When we made PuMA, we decided the recircularize all genomes at the same position (i.e., the first nt after the L1 stop codon). Since most of the older genomes in genbank recircularize somewhere upstream of E6, our positions will be offset. I hope this help!
Koenraad
On Feb 16, 2023, at 11:59 PM, Jia-Xing Yue ***@***.******@***.***>> wrote:
External Email
Dear @KVDlab<https://github.com/KVDlab>
Sorry. While testing with HPV16 and HPV18 reference genomes, we noticed that although the annotated CDS/protein sequences seems to be correct, the genomic coordinates might be wrong.
For example, in the reference annotation of HPV16 (https://www.ncbi.nlm.nih.gov/nuccore/NC_001526.4), the annotation shows>>
[gene](https://www.ncbi.nlm.nih.gov/nuccore/NC_001526.4?from=1892&to=2989) 1892..2989
/gene="E2"
/locus_tag="HpV16gp4"
/db_xref="GeneID:[1489080](https://www.ncbi.nlm.nih.gov/gene/1489080)"
[CDS](https://www.ncbi.nlm.nih.gov/nuccore/NC_001526.4?from=1892&to=2989) 1892..2989
/gene="E2"
/locus_tag="HpV16gp4"
/note="E2. Plays a role in the initiation of viral DNA
replication. Forms E1-E2 dimer with replication protein
E1. The E1-E2 complex binds to the replication origin
which contains binding sites for both proteins."
/codon_start=1
/product="regulatory protein E2"
/protein_id="[NP_041328.1](https://www.ncbi.nlm.nih.gov/protein/9627106)"
/db_xref="GeneID:[1489080](https://www.ncbi.nlm.nih.gov/gene/1489080)"
/translation="METLCQRLNVCQDKILTHYENDSTDLRDHIDYWKHMRLECAIYY
KAREMGFKHINHQVVPTLAVSKNKALQAIELQLTLETIYNSQYSNEKWTLQDVSLEVY
LTAPTGCIKKHGYTVEVQFDGDICNTMHYTNWTHIYICEEASVTVVEGQVDYYGLYYV
HEGIRTYFVQFKDDAEKYSKNKVWEVHAGGQVILCPTSVFSSNEVSSPEIIRQHLANH
PAATHTKAVALGTEETQTTIQRPRSEPDTGNPCHTTKLLHRDSVDSAPILTAFNSSHK
GRINCNSNTTPIVHLKGDANTLKCLRYRFKKHCTLYTAVSSTWHWTGHNVKHKSAIVT
LTYDSEWQRDQFLSQVKIPKTITVSTGFMSI"
However, the annotation from PUMA suggests:
E2 start and stop position:
3506,4603
E2 sequence:
atggagactctttgccaacgtttaaatgtgtgtcaggacaaaatactaacacattatgaaaatgatagtacagacctacgtgaccatatagactattggaaacacatgcgcctagaatgtgctatttattacaaggccagagaaatgggatttaaacatattaaccaccaggtggtgccaacactggctgtatcaaagaataaagcattacaagcaattgaactgcaactaacgttagaaacaatatataactcacaatatagtaatgaaaagtggacattacaagacgttagccttgaagtgtatttaactgcaccaacaggatgtataaaaaaacatggatatacagtggaagtgcagtttgatggagacatatgcaatacaatgcattatacaaactggacacatatatatatttgtgaagaagcatcagtaactgtggtagagggtcaagttgactattatggtttatattatgttcatgaaggaatacgaacatattttgtgcagtttaaagatgatgcagaaaaatatagtaaaaataaagtatgggaagttcatgcgggtggtcaggtaatattatgtcctacatctgtgtttagcagcaacgaagtatcctctcctgaaattattaggcagcacttggccaaccaccccgccgcgacccataccaaagccgtcgccttgggcaccgaagaaacacagacgactatccagcgaccaagatcagagccagacaccggaaacccctgccacaccactaagttgttgcacagagactcagtggacagtgctccaatcctcactgcatttaacagctcacacaaaggacggattaactgtaatagtaacactacacccatagtacatttaaaaggtgatgctaatactttaaaatgtttaagatatagatttaaaaagcattgtacattgtatactgcagtgtcgtctacatggcattggacaggacataatgtaaaacataaaagtgcaattgttacacttacatatgatagtgaatggcaacgtgaccaatttttgtctcaagttaaaataccaaaaactattacagtgtctactggatttatgtctatatga
E2 translated sequence:
METLCQRLNVCQDKILTHYENDSTDLRDHIDYWKHMRLECAIYYKAREMGFKHINHQVVPTLAVSKNKALQAIELQLTLETIYNSQYSNEKWTLQDVSLEVYLTAPTGCIKKHGYTVEVQFDGDICNTMHYTNWTHIYICEEASVTVVEGQVDYYGLYYVHEGIRTYFVQFKDDAEKYSKNKVWEVHAGGQVILCPTSVFSSNEVSSPEIIRQHLANHPAATHTKAVALGTEETQTTIQRPRSEPDTGNPCHTTKLLHRDSVDSAPILTAFNSSHKGRINCNSNTTPIVHLKGDANTLKCLRYRFKKHCTLYTAVSSTWHWTGHNVKHKSAIVTLTYDSEWQRDQFLSQVKIPKTITVSTGFMSI
Best,
Jia-Xing
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Dear @KVDlab, I see. Make sense. Thank you very much! On another note, after making more tests with puma, we noticed that:
We were wondering if further updates could be applied to make corresponding improvements. FYI: And this is the HPV18 L1 protein sequence annotated by PUMA using the same input genome sequnce: Best, |
Hey,
Not sure why you are reopening, but if it is due to the E4 and L1 I can explain below
1) As we describe in the PuMA paper, the biological evidence suggests that L1 uses a Met start codon that is typically 4 aa upstream of a conserved W.
2) We do not think ‘E4’ is a protein. We annotate E1^E4, not the E4 exon alone.
Hope that helps
On Feb 26, 2023, at 5:30 PM, Jia-Xing Yue ***@***.******@***.***>> wrote:
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Reopened #2<#2>.
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Dear @KVDlab, Many thanks for the explanation! Very helpful! Best, |
Hello, we were trying to run puma via docker but encountered the following error. Could you please help us to diagnose what might be the cause. Thanks in advance!
Command:
Error message:
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