ShapeMapper run failed while MutationCounter_modified
amkilar opened this issue · 4 comments
Hello,
I'm trying to run fastq files with ShapeMapper2 and for raw data it works perfectly. However, if I first run preprocessing with FASTX (trimming and quality-based filtering) and then Shapemapper, it fails without any specified error always very close to the end (97-100%) of MutationCounter_modified calculation.
Primarily, I thought that it might be a problem with the different lengths of the reads, but made them the same length and it didn't solve the issue.
I would appreciate any help.
Sorry for not replying sooner. Did you find a solution to this issue?
Unfortunately, the problem persists also after processing raw reads with TRIMMOMATIC, instead of FASTX.
Again, I checked for different numbers of reads of R1 and R2, but they are the same. Shapemapper2 output look as follow (without any specific error):
Later, I tried to make all reads within R1 and R2 of the same length, but the problem with Shapemapper2 persisted.
Sorry, I can't say exactly what is happening here. Failing without error makes this very hard to diagnose.
You said that the pipeline works fine for untrimmed/unfiltered reads. If that is the only thing that is changing, it makes me think that Shapemapper2 is taking issue with the format of your input reads. However, usually it will catch errors in format long before it gets to MutationCounter.
It might be that it Shapemapper2 is failing with some interaction between modules. Try running the pipeline without --render-flowchart --render-mutations --per-read-histograms --output-processed-reads --output-aligned-reads --output-parsed-mutations --output-counted-mutations.
If that doesn't work, check your fastq files. Check the number of lines. Check the fastq format at the top and bottom of the file using head/tail. Fastq file names should match exactly save the R1/R2 field. There should be no other fastq files in the folder. The 3rd line of each fastq entry should contain only a '+'. Run FASTQC on pre/post-FASTX files to make sure there aren't any glaring issues with the sequences or qualities. (this is good practice in general before running Shapemapper2).
Let me know how this goes and if you find out anything.
Thank you for your response and help!
My trimmomatic run resulted in creating trimmed reads and unpaired reads. It seems to cause me further issues with Shapemapper2. I removed unpaired reads from the folder, and it solved the problem.