sbatch: error: ClusterName needs to be specified

[hrydbeck]

Description of the bug

Command output: sbatch: s_p_parse_file: file "/cfs/klemming/home/h/halfdan/.atp/x86_64/slurm.conf" is empty sbatch: error: ClusterName needs to be specified sbatch: fatal: Unable to process configuration file

There also the "join mismatch errors". Not sure what they mean and what to do about them.

Command used and terminal output

nextflow run nf-core/raredisease -r "patch" -profile test,singularity -c ./halfdan_pdc.config --outdir test_rev_patch_out --project naiss2024-22-481

ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman)'

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

Command executed:

  sbatch .command.run

Command exit status:
  1

Command output:
  sbatch: s_p_parse_file: file "/cfs/klemming/home/h/halfdan/.atp/x86_64/slurm.conf" is empty
  sbatch: error: ClusterName needs to be specified
  sbatch: fatal: Unable to process configuration file

Work dir:
  /cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/67/b9e62c364740b1914e6d3b556613a4

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

 -- Check '.nextflow.log' file for details
Join mismatch for the following entries:
- key=[id:earlycasualcaiman, sample:earlycasualcaiman, sex:1, phenotype:1, paternal:0, maternal:0, case_id:justhusky, num_lanes:1, read_group:'@RG\tID:earlycasualcaiman\tPL:illumina\tSM:earlycasualcaiman', single_end:false, interval:18, nr_of_intervals:24] values=
- key=[id:earlycasualcaiman, sample:earlycasualcaiman, sex:1, phenotype:1, paternal:0, maternal:0, case_id:justhusky, num_lanes:1, read_group:'@RG\tID:earlycasualcaiman\tPL:illumina\tSM:earlycasualcaiman', single_end:false, interval:Y, nr_of_intervals:24] values=


Join mismatch for the following entries: key=[id:slowlycivilbuck, sample:slowlycivilbuck, sex:2, phenotype:1, paternal:0, maternal:0, case_id:justhusky, num_lanes:1, read_group:'@RG\tID:slowlycivilbuck\tPL:illumina\tSM:slowlycivilbuck', single_end:false] values=


Join mismatch for the following entries: key=[id:slowlycivilbuck, sample:slowlycivilbuck, sex:2, phenotype:1, paternal:0, maternal:0, case_id:justhusky, num_lanes:1, read_group:'@RG\tID:slowlycivilbuck\tPL:illumina\tSM:slowlycivilbuck', single_end:false] values=


Join mismatch for the following entries:
- key=[id:hugelymodelbat, sample:hugelymodelbat, sex:1, phenotype:2, paternal:earlycasualcaiman, maternal:slowlycivilbuck, case_id:justhusky, num_lanes:1, read_group:'@RG\tID:hugelymodelbat\tPL:illumina\tSM:hugelymodelbat', single_end:false, interval:18, nr_of_intervals:24] values=[/cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/f3/01448e5b4ed6f86071121c2444a150/hugelymodelbat_18.bam, /cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/30/f22103ef34445c0e8c9aa09dbc8a2d/hugelymodelbat_18.bam.bai]
- key=[id:hugelymodelbat, sample:hugelymodelbat, sex:1, phenotype:2, paternal:earlycasualcaiman, maternal:slowlycivilbuck, case_id:justhusky, num_lanes:1, read_group:'@RG\tID:hugelymodelbat\tPL:illumina\tSM:hugelymodelbat', single_end:false, interval:15, nr_of_intervals:24] values=[/cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/2d/e7bc12360be18014222e27419ba88a/hugelymodelbat_15.bam, /cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/d0/129ef8c31802921bf353617711dbc1/hugelymodelbat_15.bam.bai]
- key=[id:hugelymodelbat, sample:hugelymodelbat, sex:1, phenotype:2, paternal:earlycasualcaiman, maternal:slowlycivilbuck, case_id:justhusky, num_lanes:1, read_group:'@RG\tID:hugelymodelbat\tPL:illumina\tSM:hugelymodelbat', single_end:false, interval:16, nr_of_intervals:24] values=[/cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/c1/0534182bb256268fe3024349162409/hugelymodelbat_16.bam, /cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/bd/bdda560ceca42356df57c542069e34/hugelymodelbat_16.bam.bai]
- key=[id:slowlycivilbuck, sample:slowlycivilbuck, sex:2, phenotype:1, paternal:0, maternal:0, case_id:justhusky, num_lanes:1, read_group:'@RG\tID:slowlycivilbuck\tPL:illumina\tSM:slowlycivilbuck', single_end:false, interval:15, nr_of_intervals:24] values=[/cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/5e/61abfde9e7dc7f611ad0c1d9a34afe/slowlycivilbuck_15.bam, /cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/f9/fc526c2b4db24eac2eaa7701d0e5c4/slowlycivilbuck_15.bam.bai]
- key=[id:hugelymodelbat, sample:hugelymodelbat, sex:1, phenotype:2, paternal:earlycasualcaiman, maternal:slowlycivilbuck, case_id:justhusky, num_lanes:1, read_group:'@RG\tID:hugelymodelbat\tPL:illumina\tSM:hugelymodelbat', single_end:false, interval:14, nr_of_intervals:24] values=[/cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/11/cd51089cad958a77fec46f6de17b4b/hugelymodelbat_14.bam, /cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/95/a9640636e8ba1af51d7ec40a5d485d/hugelymodelbat_14.bam.bai]
- key=[id:slowlycivilbuck, sample:slowlycivilbuck, sex:2, phenotype:1, paternal:0, maternal:0, case_id:justhusky, num_lanes:1, read_group:'@RG\tID:slowlycivilbuck\tPL:illumina\tSM:slowlycivilbuck', single_end:false, interval:16, nr_of_intervals:24] values=[/cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/77/602fa0753ed842720e924f0c739478/slowlycivilbuck_16.bam, /cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/84/6ded015e094e8f0128d3720d678fc6/slowlycivilbuck_16.bam.bai]
- key=[id:hugelymodelbat, sample:hugelymodelbat, sex:1, phenotype:2, paternal:earlycasualcaiman, maternal:slowlycivilbuck, case_id:justhusky, num_lanes:1, read_group:'@RG\tID:hugelymodelbat\tPL:illumina\tSM:hugelymodelbat', single_end:false, interval:11, nr_of_intervals:24] values=[/cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/0e/9f931f21a24da9085daaf0946b1572/hugelymodelbat_11.bam, /cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/47/4bfa5e665e1b9d2178cbec7782c2e7/hugelymodelbat_11.bam.bai]
- key=[id:slowlycivilbuck, sample:slowlycivilbuck, sex:2, phenotype:1, paternal:0, maternal:0, case_id:justhusky, num_lanes:1, read_group:'@RG\tID:slowlycivilbuck\tPL:illumina\tSM:slowlycivilbuck', single_end:false, interval:17, nr_of_intervals:24] values=[/cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/af/46e9f05874c8ab71e407805eb98df5/slowlycivilbuck_17.bam, /cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/2c/a6e9723a62a9d35649afab2593c1d3/slowlycivilbuck_17.bam.bai]
- key=[id:hugelymodelbat, sample:hugelymodelbat, sex:1, phenotype:2, paternal:earlycasualcaiman, maternal:slowlycivilbuck, case_id:justhusky, num_lanes:1, read_group:'@RG\tID:hugelymodelbat\tPL:illumina\tSM:hugelymodelbat', single_end:false, interval:12, nr_of_intervals:24] values=[/cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/b6/277fdddb3637d780775c2454b91e20/hugelymodelbat_12.bam, /cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/b5/7a5fc98e3dbeb2a51a82e555214b85/hugelymodelbat_12.bam.bai]
- key=[id:slowlycivilbuck, sample:slowlycivilbuck, sex:2, phenotype:1, paternal:0, maternal:0, case_id:justhusky, num_lanes:1, read_group:'@RG\tID:slowlycivilbuck\tPL:illumina\tSM:slowlycivilbuck', single_end:false, interval:18, nr_of_intervals:24] values=[/cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/a9/f0b37d5b2cf6e87f6da9fff68645ae/slowlycivilbuck_18.bam, /cfs/klemming/projects/supr/naiss2024-23-348/nfc_rd/work/46/3fe622a9d84d1455cf9e1f8e23fbcd/slowlycivilbuck_18.bam.bai]
(more omitted)

Relevant files

nextflow_failed_to_submit_to_scheduler.log

System information

Nextflow version 23.10.1 HPC,PDC-Dardel slurm Singularity SUSE Linux Enterprise Server 15 SP5 nfc-rd version "patch"