Comments (11)
Hi! Thanks for reporting this. Looks like the code has some trouble writing the results to a file. My first guesses would be:
- the actual string of [RAW DATA] or [TE] contains some symbol that turns it into an invalid filepath, e.g.
/
or a space? Seems odd though if this happens for all TEs - Permissions of the directory that it tries to write to could be another issue, but then I would expect a different Error.
Would you mind sharing the command used to run deviaTE? And maybe double-check that the library of TE sequences is a valid fasta file?
cheers
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Hi! Glad that your original issue was solved. deviaTE should probably check for such situations itself to be fair. I'll implement a fix for that.
Concerning your second question: If there are no reads mapping to a TE reference, then deviaTE should give a message like this:
...
******************** Analysis
Starting analysis of [TE] in [BAM-FILE]..
No reads mapped to the specified reference sequence
...
The program should then exit without producing any output. Hope this helps!
Lukas
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I added a check to replace invalid characters in TE names, which should prevent the original error (10d2b70). I'm not going to make a new release of the package at this point. But if you would like to make use of this change, you can replace the updated code file on your computer (bin/deviaTE_analyse
in this repository). In case you installed the tool via conda, it should be located somewhere along the lines of:
~/miniconda3/envs/deviaTE_env/bin/deviaTE_analyse
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No problem! Forgot to mention that the fix is basically replacing problematic characters with dashes, so that the analysis can proceed without issues.
The message about "no annotations" refers to the optional parameter --annotation
. This can be used to provide GFF3 files with annotations of the TE sequences, e.g. the location of CDS and other defined genetic elements. These will mainly be used in the visualisation, e.g. at the bottom of this one:
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That's a tricky one. I think a two-pronged approach might be worth considering in this case.
- Repository-based: Try and collect all relevant sequences from already existing TE databases for the species (and related ones) that you are studying
- De-novo assembly of repeats from raw reads: There are quite a few tools that can do this, but I don't know for which species and coverage they are suitable. Some that come to my mind are RepeatExplorer (https://pubmed.ncbi.nlm.nih.gov/23376349/), dnaPipeTE (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4419797/), REPdenovo (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792456/).
You could then, for example, use a combined library of TE sequences from these with deviaTE to quantify the TE content.
A possibly helpful review with lots of links to databases & tools: https://www.nature.com/articles/s41576-018-0050-x#ref-CR77
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Related Issues (15)
- y
- Genome Size HOT 4
- Diversity Estimates
- IndexError: list index out of range HOT 7
- more than one primary alignment & unsupported operand type(s) for +: 'NoneType' and 'str' HOT 1
- --input_fq_dir contains .fq files HOT 1
- various errors after conda installation HOT 5
- condo create problems with samtools HOT 2
- Idea for walkthrough: additional information on how to process paired reads HOT 2
- Error during deviaTE_prep step: ValueError: more than one primary alignment
- Error in install.packages("data.table", repos = rep) : unable to install packages HOT 7
- Single_copy_genes, ValueError: invalid contig Gene1 HOT 2
- Stuck on prep stage HOT 3
- Issue with --input_bam_dir HOT 2
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