Hi everyone,
I’m having some troubles understanding what I’ve done wrong.
I want to assembly a transcriptome from different samples retrieved from the NCBI. Since I had several forward and reverse reads I used the concatenate tool to obtain one dataset for all the forward reads and one for all the reverse reads. At this point I’ve built a collection (with the build dataset pair function, named: All sequences-cleaned ) and I’ve performed trimmomatic and FASTQC (both ran well).
After that I ran Trinity with these parameters:
|Are you pooling sequence datasets?|No|
|Paired or Single-end data?|unmerged_paired_collection|
|FASTA/FASTQ dataset collection with R1/R2 pair| 142: All sequences-cleaned
This gave me this error:
Execution resulted in the following messages:
Fatal error: Exit code 2 ()
Detected Common Potential Problems
The tool was executed with one or more empty input datasets. This frequently results in tool errors due to problematic input choices.
Hi @Letizia_Iuffrida
Trinity can pull files for a single job, hence no need for concatenation.
Maybe try assembly on a single set of data (F and R reads). Does it work? If the answer is positive, try Trinity with with pulling data set to Yes. I completed a test Trinity job on Galaxy Europe on several samples using pulling option, and don’t see any issue with the tool.
As for the error message:
The tool was executed with one or more empty input datasets.
I don’t know if it is generic (aka generated for any failed job) or specific, but please preview the input files.
Kind regards,
Igor
Thanks @igor for the reply, I used the concatenate tool to simplify the previous preparation since I have more than ten samples and it’s easier for me to have just one dataset with all the R reads and one for the F reads. Anyway, I’ll try to run Trinity with a single run.
I checked the input files and they seems ok to me.
I was thinking, could the problem be related to the fact that I’m trying to assemble about 45-50 GB and maybe it’s too heavy for the server? I was reading in the forum that maybe this is the problem…
Hi @Letizia_Iuffrida
Do you mean total size of gzipped FASTQ files is 50 GB? It might be too big, but you need a feedback from the server admin. I assume, in silico normalization of reads was enabled. Maybe consider using khmer: Normalize By Median on merged files before Trinity.
Kind regards,
Igor