Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/c3se/NOBACKUP/users/johnhe/miniconda3/envs/rna_seq_py2.7/etc/tmp
N E X T F L O W  ~  version 0.26.3
Launching `SciLifeLab/NGI-RNAseq` [admiring_cuvier] - revision: 4e083df3c8 [master]
=========================================
 NGI-RNAseq : RNA-Seq Best Practice v1.4dev
=========================================
Run Name       : admiring_cuvier
Reads          : /c3se/NOBACKUP/users/johnhe/rnaseq/raw/*{1,2}_001.fastq.gz
Data Type      : Paired-End
Genome         : R64-1-1
Strandedness   : None
Trim R1        : 0
Trim R2        : 0
Trim 3' R1     : 0
Trim 3' R2     : 0
Aligner        : STAR
STAR Index     : /c3se/NOBACKUP/users/johnhe/referencegenome/star
GTF Annotation : /c3se/NOBACKUP/users/johnhe/referencegenome/genes.gtf
BED Annotation : /c3se/NOBACKUP/users/johnhe/referencegenome/genes.bed12
Save Reference : Yes
Save Trimmed   : No
Save Intermeds : No
Output dir     : /c3se/NOBACKUP/users/johnhe/rnaseq/results3
Working dir    : /c3se/NOBACKUP/users/johnhe/rnaseq/raw/work
Container      : [:]
Pipeline Release: master
Current home   : /c3se/users/johnhe/Hebbe
Current user   : johnhe
Current path   : /c3se/NOBACKUP/users/johnhe/rnaseq/raw
R libraries    : false
Script dir     : /c3se/users/johnhe/Hebbe/.nextflow/assets/SciLifeLab/NGI-RNAseq
Config Profile : hebbe
UPPMAX Project : SNIC2017-1-89
=========================================
[warm up] executor > slurm
[a9/9377f8] Submitted process > fastqc (NC1_S1_L002_R)
[warm up] executor > local
[32/02f101] Submitted process > trim_galore (NC1_S1_L002_R)
[bb/8fef69] Submitted process > star (NC1_S1_L002_R1_001)
          Passed alignment > star (NC1_S1_L002_R1_001)   >> 88.74% <<
[e5/5c47b9] Submitted process > rseqc (NC1_S1_L002_R1_001AlignedByCoord.out)
[b3/818d42] Submitted process > preseq (NC1_S1_L002_R1_001AlignedByCoord.out)
[35/e80538] NOTE: Error submitting process 'genebody_coverage (NC1_S1_L002_R1_001AlignedByCoord.out)' for execution -- Error is ignored
[d9/70a986] Submitted process > featureCounts (NC1_S1_L002_R1_001AlignedByCoord.out)
ERROR ~ Error executing process > 'markDuplicates (NC1_S1_L002_R1_001AlignedByCoord.out)'

Caused by:
  Failed to submit process to grid scheduler for execution

Command executed:

  sbatch .command.run

Command exit status:
  1

Command output:
  sbatch: error: rejecting job, too much memory requested for 2 cores. You must use -C MEMXXX or increase number of requested cores instead of using --mem: pn_min_memory = 16384
  sbatch: error: Batch job submission failed: Invalid generic resource (gres) specification

Work dir:
  /c3se/NOBACKUP/users/johnhe/rnaseq/raw/work/9e/52845c74971ad09a126e27b9bfcdb9

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit