Comments (4)
For now there is only a hacky ways to todo this. You could start your job and immediately stop it.
Now call:
plass createdb yourorfs.faa orfs
touch tmp/latest/nucl_6f_start
touch tmp/latest/aa_6f_start
touch tmp/latest/nucl_6f_long
touch tmp/latest/aa_6f_long
ln -s orfs tmp/latest/aa_6f_start_long
ln -s orfs.index tmp/latest/aa_6f_start_long.index
ln -s orfs.dbtype tmp/latest/aa_6f_start_long.dbtype
ln -s orfs_h tmp/latest/aa_6f_start_long_h
ln -s orfs_h.index tmp/latest/aa_6f_start_long_h.index
ln -s orfs_h.dbtype tmp/latest/aa_6f_start_long_h.dbtype
Now restart your run by calling the initial plass
command.
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Thanks Martin!
I have a couple of hundreds of metagenomes to assemble. For now, I will try to modify the PLASS assembler workflow and add these steps and see if it works.
Antonio
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Hi Martin
I modified assembledb.sh to include the hack you suggested and seems to works correctly. I can reduce the number of assembled proteins with the default NN filter value.
if notExists "${TMP_PATH}/nucl_6f_start"; then
touch "${TMP_PATH}"/nucl_6f_start
fi
if notExists "${TMP_PATH}/aa_6f_start"; then
touch "${TMP_PATH}"/aa_6f_start
fi
if notExists "${TMP_PATH}/nucl_6f_long"; then
touch "${TMP_PATH}"/nucl_6f_long
fi
if notExists "${TMP_PATH}/aa_6f_start_long"; then
touch "${TMP_PATH}"/aa_6f_long
ln -s "${INPUT}" "${TMP_PATH}"/aa_6f_start_long
ln -s "${INPUT}".index "${TMP_PATH}"/aa_6f_start_long.index
ln -s "${INPUT}".dbtype "${TMP_PATH}"/aa_6f_start_long.dbtype
fi
if notExists "${TMP_PATH}/aa_6f_start_long_h"; then
ln -s "${INPUT}"_h "${TMP_PATH}"/aa_6f_start_long_h
ln -s "${INPUT}"_h.index "${TMP_PATH}"/aa_6f_start_long_h.index
ln -s "${INPUT}"_h.dbtype "${TMP_PATH}"/aa_6f_start_long_h.dbtype
fi
Some numbers:
file format type num_seqs sum_len min_len avg_len max_len
orfs_aa.faa FASTA Protein 2,912 82,008 17 28.2 84
orfs_nt.faa FASTA Protein 4,236 130,973 21 30.9 91
raw.faa FASTA Protein 5,609 173,304 21 30.9 92
Where orfs_aa are the predicted ORFs in aa, orfs_nt are the predicted ORFs in nt and raw are the raw reads.
These are ancient reads (short and damaged), and using the default workflow, I was getting many proteins that I believe might be spurious.
I will rerun all metagenomes with the modified workflow and compare the outcome in terms of annotations and other parameters I calculate. I keep you posted.
Thank you very much
Antonio
from plass.
Thank you for sharing the data. I think the spurious proteins might be introduced by our change to add complete short Orfs. Even if they were not assembled. E.g. if the is a complete Orf encoded on one read then we add them to the final result. We try to filter these out with the NN, but the NN seems to not always be able to remove them.
Do you see that many of the spurious proteins are short?
from plass.
Related Issues (20)
- Use Plass for euk metagenomics data HOT 2
- The output file is empty HOT 1
- Segmentation fault translatenucs HOT 2
- Some Issues about the length of protein sequences HOT 2
- Empty (len:0) sequences in plass output HOT 4
- Issue with Docker image soedinglab/plass:latest HOT 2
- Use PLASS in metatranscriptomic data HOT 5
- Update MMseqs2 submodule
- Install issues HOT 6
- Paired read prediction - mergereads failed HOT 3
- Quantification
- High level of duplicated protein sequences HOT 1
- mmseqs extractorfs can tranlate orfs but CLI does not allow to specify tranlation table HOT 2
- general question to gauge dev opinion/advice on selecting proteins for gene phylogenies HOT 2
- Quality trimming reads? HOT 2
- Alternative codon table HOT 2
- Insights needed for comparison with other assemblers HOT 1
- Penguin: no assembled contigs
- Data Access HOT 1
- Feature requests: (Un)trusted contigs and mixed read types support
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