Process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/genomic.fna) terminated with an error exit status ( 255)

[abu85]

Description of the bug

I a running a rnaseq data on nfcore rnaseq for DEG analyses on uppmax. But I have problem here, its cancelled every time in the following step. why? how to overcome this ?

NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA

Command used and terminal output

$nextflow run nf-core/rnaseq \
--input /proj/snic2021-xx-xxx/nobackup/rna_seq/nxf/test_sample_sheet.csv \
--reads /proj/snic2021-xx-xxx/nobackup/rna_seq/nxf/input_files/*_R{1,2}_001.fastq.gz \
-profile uppmax,singularity \
--max_cpus 20 \
--max_memory 128.GB \
--project snic2021-xx-xxx \
-bg \
-resume \
--fasta /proj/snic2021-xx-xxx/nobackup/rna_seq/nxf/genome/genomic.fna \
--gtf /proj/snic2021-xx-xxx/nobackup/rna_seq/nxf/genome/genomic.gtf \
--aligner hisat2 \
--outdir /proj/snic2021-xx-xxx/nobackup/rna_seq/nxf/new_test/results > rnaseq_test_run_log.txt

Relevant files

[1d/e63985] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/genomic.fna) [57/cd6080] Submitted process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:HISAT2_BUILD (genomic.fna) [e6/40d2f9] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (Susceptible-21-Healthy-Young-3) [f5/c564d6] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:FASTQC (Susceptible-28-Healthy-Young-3) [09/50cddd] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (Susceptible-28-Healthy-Young-3) [39/736c6a] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (Susceptible-21-Healthy-Young-3) Error executing process > 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/genomic.fna)'

Caused by: Process NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/genomic.fna) terminated with an error exit status ( 255)

Command executed:

rsem-prepare-reference \ --gtfgenomic_genes.gtf \ --num-threads 12 \ \ rsem/genomic.fna \ rsem/genome

cp rsem/genome.transcripts.fa .

cat <<-END_VERSIONS > versions.yml "NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTSFASTA": rsem: $(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g") star: $(STAR --version | sed -e "s/STAR//g") END_VERSIONS

Command exit status: 255

Command output: rsem-extract-reference-transcripts rsem/genome 0 genomic_genes.gtf None 0 rsem/genomic.fna "rsem-extract-reference-transcripts rsem/genome 0 genomic_genes.gtf None 0 rsem/genomic.fna" fa iled! Plase check if you provide correct parameters/options for the pipeline!

Command error: WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container The reference contains no transcripts!

Work dir: /crex/proj/snic2021-xx-xxx/nobackup/rna_seq/nxf/new_test/work/1d/e639850b75ff81126409c76b562c36

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

Execution cancelled -- Finishing pending tasks before exit`

System information

N E X T F L O W ~ version 21.10.6 nf-core/rnaseq v3.6

UPPMAX

[Nico-FR]

Hi have the same issue, did you solve it?

[abu85]

No. So I changed the alignment option I did not use STAR or RSEM. I have used SALMON instead of STAR or RSEM?