TransPi
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PalMuc
TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly
I'm getting the following error message while running the full analysis. Error executing process > 'normalize_reads (control_R)' Caused by: Process `normalize_reads (control_R)` terminated with an error exit status (127) Command...
Hi! I was running the onlyAnn mode through the singularity. However, there is an error saying that: ``` Command error: cp: can't stat '/gene_annotation/TransPi/DBs/sqlite_db/*.sqlite': No such file or directory ```...
The `precheck_TransPi.sh` script fails to download the UniProt Metazoa database due to changes to the API. This is what comes back from the download command: ``` $ curl -o uniprot_metazoa_33208.fasta.gz...
Hi, How does the pipeline deals with the direction of sequencing, is there a way to inform it (for example, if it is stranded)? If there is a way to...
Hi, I apologize for my frequent contacts. When the runninfg of SOS_busco.py in process busco4_dist, I got following error, ``` Command error: Traceback (most recent call last): File "/mnt/data/software/TransPi/bin/SOS_busco.py", line...
Thanks for providing this nice pipeline! I run an analysis with the following command: ./nextflow run TransPi.nf --all --maxReadLen 143 --k 25,35,55,75,85 --reads '/media/server2/Data_2Gb/Melongena/Data/Trimmed/Trimmed/provaR673_HP/R673HP831val_R[1,2].fastq.gz' --outdir /media/server2/Data_2Gb/Melongena/TransPi_R673_HP8 -profile docker --skipQC Everthing...
The Dockerfile tries to copy transpi_env.yml and build a conda environment from it, but no such file seems to exist in this repo. Where can I access this file?
Hi there, I've been trying to use TransPi (love the concept and the benchmarking in the paper looks great!) to re-assemble some older public datasets. Running on an interactive slurm...
Hello, I am trying to install and use signalP. Which version of signalP works with TransPi? I tried installing v6 and v5. I get similar errors as below , so...
Hi, I've noticed that for some datasets the TransPi (conda controlled) seems to sort of get stuck in the Trinity assembly phase. Basically the pipeline stays in the `salmon index`...
