DEA error

[BobW4ng]

Hello Mr.Zhang, For some reason, I am getting an error in the DEA steps. Error in tximport(files, type = "salmon", txOut = TRUE, countsFromAbundance = "no") : all(file.exists(files)) is not TRUE Calls: DEA -> tximport -> stopifnot Execution halted [Mon Sep 12 11:16:57 2022] Error in rule DEA: jobid: 1 output: output/WT/trans/dea/DEA/transcript-level/dea_wt_ko.tsv, output/WT/trans/dea/DEA/transcript-level/deg_wt_ko.tsv, output/WT/trans/dea/DEA/gene-level/dea_wt_ko.tsv, output/WT/trans/dea/DEA/gene-level/deg_wt_ko.tsv

RuleException: CalledProcessError in line 40 of /mnt/d/RNAseq/qhd2/workflow/dea_trans.rules: Command ' set -euo pipefail; Rscript scripts/dea_trans.R ' returned non-zero exit status 1. File "/mnt/d/RNAseq/qhd2/workflow/dea_trans.rules", line 40, in __rule_DEA File "/home/wbc/miniconda3/envs/ranseqSnakemake/lib/python3.6/concurrent/futures/thread.py", line 56, in run Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /mnt/d/RNAseq/qhd2/.snakemake/log/2022-09-12T110512.827029.snakemake.log DEA is done! Visualization is not required and RASflow is done! Building DAG of jobs... Nothing to be done. Complete log: /mnt/d/RNAseq/qhd2/.snakemake/log/2022-09-12T110510.915007.snakemake.log

Any help is appreciated. Thank you.

[zhxiaokang]

As I can understand from the error message,

Error in tximport(files, type = "salmon", txOut = TRUE, countsFromAbundance = "no") :
all(file.exists(files)) is not TRUE

it seems that the quantity files (output from salmon) are not there, please check whether you have output/WT/trans/quant/[sample]/quant.sf

[BobW4ng]

thank you sir！

[zhxiaokang]

No problem. I will then close it. Feel free to reopen it if the same error remains there. And also feel free to open new issues if some new error occurs.