Open giriarteS opened 2 years ago
Hi @giriarteS,
We haven't tested modpolish on fungi yet. Have you ever successfully run the original homopolish polish
? If so, can you give us your fasta genome and fastq reads for debugging? modpolish
is a new feature for genomes extensively edited by modifications untrained in the ONT basecalling. If your genomes are not extensively modified, you don't need to run modpolish
.
I run homopolish polish but I got the following for each contig: python3 /mnt/DATA/git_repos/homopolish/homopolish.py polish -a medaka/consensus.fasta -m R9.4.pkl -s /mnt/DATA/git_repos/homopolish/fungi.msh -o homopolish -t 50
[2022/05/25 17:24] INFO: Stage: Select closely-related genomes TIME Select closely-related genomes: 0 MINS 0 SECS. This contig contig_75 closely-related genome is less than 5, not to polish... [2022/05/25 17:24] INFO: RUN-ID: contig_197
I successfully run homopolish polish: homopolish.py polish -a medaka/consensus.fasta -m R9.4.pkl -l reference/F.verticillioides/GCF_000149555.1_ASM14955v1_genomic.fna.gz -o homopolish -t 25
We found the error was due to an insufficient number of related genomes (<5), a bug in modpolish but not original homopolish. It looks to us there are six in GenBank but only one in RefSeq. Therefore, as you have done, the local db option -l
can specify the related genomes downloaded on your own. However, I would suggest you concatenate all the six related genomes into one fasta not just provided only one.
I polished my genomes with several rounds of racon, then medaka, then homopolish. If I want to use illumina reads to polish with Pilon, should homopolish be run before or after pilon?
It was trained on Medaka-polished genomes. We would recommend running homopolish right after Medaka and then followed by pilon.
Can modpolish be used after racon+medaka? I am trying to polish my assembly (flye+6 rounds of racon+medaka) with modpolish but I get the following error: "python3 /mnt/DATA/git_repos/homopolish/homopolish.py modpolish -a medaka/consensus.fasta -q /mnt/Backup/Genomes_test/raw_dna/minion/F.verticillioides/MRC826E/MRC826E_trim_fastq.gz -s /mnt/DATA/git_repos/homopolish/fungi.msh -o homopolish -t 50
Downloaded GCA_003316995.2_ASM331699v2_genomic.fna.gz Downloaded GCA_003316975.2_ASM331697v2_genomic.fna.gz Downloaded GCA_011035275.1_ASM1103527v1_genomic.fna.gz Downloaded GCA_011036225.1_ASM1103622v1_genomic.fna.gz Downloaded GCA_000149555.1_ASM14955v1_genomic.fna.gz Downloaded GCF_000149555.1_ASM14955v1_genomic.fna.gz Downloaded GCA_003317015.2_ASM331701v2_genomic.fna.gz Downloaded GCA_011036015.1_ASM1103601v1_genomic.fna.gz Downloaded GCA_011036905.1_ASM1103690v1_genomic.fna.gz
load Homo
Gloria