Comments (2)
Thanks for trying out Phamb!
If you ran Vamb seperately for each coassembly, it makes sense to run Phamb seperately for each coassembly as well.
Now to your problem: It is the naming of your contigs that produce the error, specifically the "spaces" in the fasta header.
I would recommend renaming your contigs and replace spaces with "_" not only to make this parsing script work but many other bioinformatic tools do not work properly with spaces in fasta headers either.
The name change should look like this:
k141_1091919 flag=0 multi=5.9626 len=1318 -> k141_1091919_flag=0_multi=5.9626_len=1318
I
Best,
Joachim
from phamb.
Thank you very very much!!
from phamb.
Related Issues (20)
- modified header names in PHAMB HOT 4
- Versioned release package for Phamb HOT 16
- contig length HOT 1
- Update shebang lines in phamb python scripts HOT 2
- High number of bacterial genes in phamb assembled bins HOT 3
- split_contigs.py produces empty files HOT 1
- Can PHAMB output comparable performance on environmental metagenome compared to gut metagenome HOT 1
- split_contigs.py produces empty files HOT 2
- how to evaluate the bin-annotations? HOT 1
- What are the criteria of RF model HOT 2
- The predicted 'viral' number in 'vambbins_RF_predictions.txt' is inconsistent with the actual number in 'vamb_bins.1.fna'? HOT 1
- Binning question, how to use vamb? HOT 7
- 'run_RF.py' operation problem HOT 1
- how to get the file 'clusters.tsv' ?
- VAE or AAE? HOT 1
- How to Run - not in parallel - quick and dirty HOT 1
- interpret the results of RF model
- Can PHAMB be used directly for Virome analysis (enrichment of viral particles followed by sequencing) HOT 2
- category of viruses identified by PHAMB ?
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