Error while performing DenovoRNAseq.

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hello
i am new to bioinformatics when, i am performing denovoRNAseq, while runnig abundance estimate using RSEM i get a error.

/mnt/e/DenovoRNAseq/TOOLS/Trinityrnaseq-v2.6.6/util/align_and_estimate_abundance.pl --seqType fq --transcript /mnt/e/DenovoRNAseq/Trinity_output.dnv/Trinity.fasta --left trim_Treated1_1.fastq --right trim_Treated1_2.fastq --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference --output_dir /mnt/e/DenovoRNAseq/Trinity_output.dnv/RSEM_Treared1
i am using this command.

i got a error like this

if you provide correct parameters/options for the pipeline!
Error, cmd: rsem-calculate-expression --paired-end -p 4 --no-bam-output --bam bowtie.bam.for_rsem.bam /mnt/e/DenovoRNAseq/Trinity_output.dnv/Trinity.fasta.RSEM RSEM died with ret: 65280 at /mnt/e/DenovoRNAseq/TOOLS/Trinityrnaseq-v2.6.6/util/align_and_estimate_abundance.pl line 790.

kindly help me to solve this issue.
thank you.

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Welcome, @rani_pv

We’ll need more details about your error to help. Please see the banner at this forum, or here directly for the how-to. The history share link will work best for what I think is the problem.

Be sure that the history also includes the upstream steps you did to prepare the RSEM reference, and for the Trinity steps, so we can find where the original issue was introduced and offer actionable advice to fix things up.

If you are not working in Galaxy, you could considering using Galaxy instead! We have all the tools in the protocol. Ask if you have any questions about how to get started.

Let’s start there! :slight_smile:

3

Thank you so much for your response jennaj.

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