RNA-Seq pipeline fails during STAR alignment

Question

[arunprasanna83]

Hi,

I tried to run RNA-Seq pipeline in the following way:

RNA-seq -i /data/TRANSCRIPTOME/CC7_TS/CC7_Clean -o ./TEST_OUT/ -j 10 --local --DAG -m 'alignment-free,deepTools_qc' --sampleSheet samplesheet.txt CC7v2

The dry-run went well without potential errors. When I submit the job, I get the following error:

Activating conda environment: /home/nagaraap/Downloads/Softwares/Anaconda/yes/envs/549d169470e49d19b2c44ad01f335827
mktemp: failed to create directory via template ‘/data/extended//snakepipes.XXXXXXXXXX’: No such file or directory
[Thu Feb  6 16:28:34 2020]
Error in rule STAR:
    jobid: 496
    output: STAR/41C-32L120.non_rRNA.sorted.bam
    conda-env: /home/nagaraap/Downloads/Softwares/Anaconda/yes/envs/549d169470e49d19b2c44ad01f335827
    shell:
                 MYTEMP=$(mktemp -d ${TMPDIR:-/tmp}/snakepipes.XXXXXXXXXX);
                ( [ -d STAR/41C-32L120.non_rRNA ] || mkdir -p STAR/41C-32L120.non_rRNA )
                STAR --runThreadN 10   --sjdbOverhang 100   --readFilesCommand zcat  --outSAMunmapped Within --outSAMtype BAM Unsorted  --outStd BAM_Unsorted --sjdbGTFfile /ANALYSIS/DATA/4.13.AIPTIMESERIES_TRANSCRIPTOME_ANALYSIS/SnakePipe_test/Indices/annotation/genes.gtf  --genomeDir /SnakePipe_test/Indices/STARIndex/  --readFilesIn FASTQ/41C-32L120.non_rRNA_R1.fastq.gz FASTQ/41C-32L120.non_rRNA_R2.fastq.gz  --outFileNamePrefix STAR/41C-32L120.non_rRNA/41C-32L120.non_rRNA. | samtools sort -m 2G -T $MYTEMP/41C-32L120.non_rRNA -@ 10 -O bam -o STAR/41C-32L120.non_rRNA.sorted.bam -;
                rm -rf $MYTEMP  
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Job failed, going on with independent jobs.

The first line (Activating conda environment) was the one created during snakePipes createEnvs. I guess, the potential error is the second line "/data/extended//snakepipes.XXXXXXXXXX’: No such file or directory" . Apparently, I do not have a location called /data/extended. I checked the Snakefile and could not find the place where, I can modify the tmp directory to something existing. How can I resolve this ?

Thanks in advance.

Answer 1

[Devon Ryan]

Make sure to run snakePipes config to set the temp location to somewhere appropriate for you.

[arunprasanna83]

snakePipes config only gave a blank cursor and did not show any option like snakePipes info. Then I just edited the global defaults.yaml file !. Now I don't get the mktemp error. However, I get Error in STAR:

EXITING because of FATAL ERROR: Genome version is INCOMPATIBLE with current STAR version
SOLUTION: please re-generate genome from scratch with the latest version of STAR

I guess, somewhere there are two versions of star in one inside the createEnvs and another installed by me. Looks like somewhere I messed up things during installation. I will remove it and re-install and try.

[arunprasanna83]

Yes !!. That worked. I un-installed it entirely and re-installed snakePipes. Now it is working fine !