cea295933
commented
7 months ago circling back ... I can get this to run but it crashes during the DE analysis. I receive an error saying the Salmon needs to be upgraded:
ERROR ~ Error executing process > 'pipeline:differential_expression:count_transcripts (1)'
Caused by:
Process pipeline:differential_expression:count_transcripts (1) terminated with an error exit status (1)
Command executed:
salmon quant --noErrorModel -p "4" -t "ammended.ref_transcriptome" -l SF -a "WTpoly1_reads_aln_sorted.bam" -o counts mv counts/quant.sf "WTpoly1.transcript_counts.tsv" seqkit bam "WTpoly1_reads_aln_sorted.bam" 2> "WTpoly1.seqkit.stats"
Command exit status: 1
Command output: (empty)
Command error: Version Info: ### PLEASE UPGRADE SALMON ###
A newer version of salmon with important bug fixes and improvements is available.
The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience.
Sign up for the salmon mailing list to hear about new versions, features and updates at: https://oceangenomics.com/subscribe
salmon (alignment-based) v1.9.0
[ program ] => salmon
[ command ] => quant
[ noErrorModel ] => { }
[ threads ] => { 4 }
[ targets ] => { ammended.ref_transcriptome }
[ libType ] => { SF }
[ alignments ] => { WTpoly1_reads_aln_sorted.bam }
[ output ] => { counts }
Logs will be written to counts/logs [2023-11-10 20:38:24.291] [jointLog] [info] setting maxHashResizeThreads to 4 [2023-11-10 20:38:24.291] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. Library format { type:single end, relative orientation:none, strandedness:sense } [2023-11-10 20:38:24.293] [jointLog] [info] numQuantThreads = 2 parseThreads = 2 Checking that provided alignment files have consistent headers . . . done Populating targets from aln = "WTpoly1_reads_aln_sorted.bam", fasta = "ammended.ref_transcriptome" . . .done
cjw85
Ask away!
Hi, I'm trying to run wf-transcriptomes on our HPC and have questions about the best way to take advantage of multiple cpus and multiple threads. I had been using the --ntasks-per-node option but have switched to the --cpues-per-task option. Does this make a meaningful difference and/or should I use them together? We also have multiple nodes. Would it be helpful to request more than one node? For reference, one node has 2 sockets, 32 CPUs per socket, and 2 threads per CPU core. That gives 128 CPUs per node. Can wf-transcriptomes take advantage of all of this, and if so, what is the best way to do so? I am attaching below two separate sbatch scripts. One requests 1 node and 64 cpus-per-task, whereas the other simply requests --exclusive and --mem=MaxMemPerNode
Thanks!
sbatch script one
!/bin/bash
SBATCH -J Aitken_epi2me_20231110_poly
SBATCH -o Aitken_epi2me_20231110_poly.out
SBATCH --nodes=1
SBATCH --cpus-per-task=64
SBATCH -p emc
cd /work/caitken/epi2me-labs
./nextflow run epi2me-labs/wf-transcriptomes -with-trace \ --fastq /work/caitken/data/DegronNanoporeSequencing/Poly \ --ref_genome /work/caitken/data/DegronNanoporeSequencing/sacCer3/20110902_sacCer3.fa \ --ref_annotation /work/caitken/data/DegronNanoporeSequencing/sacCer3/20110902_sacCer3.gff \ --transcriptome_source reference-guided \ --ref_transcriptome /work/caitken/data/DegronNanoporeSequencing/sacCer3/20110902_sacCer3_coding.fa \ --de_analysis \ --sample_sheet /work/caitken/data/DegronNanoporeSequencing/BarcodesPoly.csv \ --out_dir /work/caitken/data/DegronNanoporeSequencing/outputPoly \ -c /work/caitken/data/DegronNanoporeSequencing/my_config.cfg
sbatch script 2
!/bin/bash
SBATCH -J Aitken_epi2me_20231110_total
SBATCH -o Aitken_epi2me_20231110_total.out
SBATCH --nodes=1
SBATCH --exclusive
SBATCH --mem=MaxMemPerNode
SBATCH -p emc
cd /work/caitken/epi2me-labs
./nextflow run epi2me-labs/wf-transcriptomes -with-trace \ --fastq /work/caitken/data/DegronNanoporeSequencing/Total \ --ref_genome /work/caitken/data/DegronNanoporeSequencing/sacCer3/20110902_sacCer3.fa \ --ref_annotation /work/caitken/data/DegronNanoporeSequencing/sacCer3/20110902_sacCer3.gff \ --transcriptome_source reference-guided \ --ref_transcriptome /work/caitken/data/DegronNanoporeSequencing/sacCer3/20110902_sacCer3_coding.fa \ --de_analysis \ --sample_sheet /work/caitken/data/DegronNanoporeSequencing/BarcodesTotal.csv \ --out_dir /work/caitken/data/DegronNanoporeSequencing/outputTotal \ -c /work/caitken/data/DegronNanoporeSequencing/my_config.cfg