```squeue -u iaperez
JOBID PARTITION ...
# sareki
Issis Abril Pérez Alvarado
02/23/2026, 11:40 AM Copy code
squeue -u iaperez
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
7138907 long sarek_te iaperez R 19:58:24 1 bc004
cat job_7138907.out
N E X T F L O W ~ version 25.10.3
Launching `<https://github.com/nf-core/sarek>` [Wang_NmIBc_BLCa_GeRMLinE_lOnG] DSL2 - revision: 20f41d1ce8 [3.7.1]
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nf-core/sarek 3.7.1
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Input/output options
input : samplesheet.csv
outdir : /storage/scratch01/groups/ce/BLCA_Germline/Results/Wang
Main options
intervals : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/intervals/Broad.human.exome.b37.interval_list
wes : true
Preprocessing
save_output_as_bam : true
General reference genome options
igenomes_base :
igenomes_ignore : true
Reference genome options
genome : GATK.GRCh37
ascat_genome : hg19
ascat_alleles : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_alleles_hg19.zip
ascat_loci : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_loci_hg19.zip
ascat_loci_gc : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/GC_G1000_hg19.zip
ascat_loci_rt : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/RT_G1000_hg19.zip
bwa : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/
chr_dir : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Sequence/Chromosomes
dbsnp : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf.gz
dbsnp_tbi : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf.gz.tbi
dict : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict
fasta : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta
fasta_fai : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai
germline_resource : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/af-only-gnomad.raw.sites.vcf.gz
germline_resource_tbi: /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/af-only-gnomad.raw.sites.vcf.gz.tbi
known_indels : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz
known_indels_tbi : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz.tbi
known_snps : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_phase1.snps.high_confidence.b37.vcf.gz
known_snps_tbi : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_phase1.snps.high_confidence.b37.vcf.gz.tbi
mappability : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem
msisensor2_models : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/MSIsensor2/models_hg19_GRCh37/
msisensorpro_scan : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/MSIsensorPro/human_g1k_v37_decoy.msisensor_scan.list
ngscheckmate_bed : /storage/scratch01/groups/ce/BLCA_Germline/GRCh37/references/Homo_sapiens/GATK/GRCh37/Annotation/NGSCheckMate/SNP_GRCh37_hg19_woChr.bed
snpeff_cache :
vep_cache :
Generic options
trace_report_suffix : 2026-02-22_16-39-18
Core Nextflow options
revision : 3.7.1
runName : Wang_NmIBc_BLCa_GeRMLinE_lOnG
containerEngine : singularity
launchDir : /home/iaperez
workDir : /storage/scratch01/groups/ce/BLCA_Germline/work
projectDir : /home/iaperez/.nextflow/assets/nf-core/sarek
userName : iaperez
profile : singularity
configFiles : /home/iaperez/.nextflow/assets/nf-core/sarek/nextflow.config, /home/iaperez/.nextflow/configs/new.cluster1.config
!! Only displaying parameters that differ from the pipeline defaults !!
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* The pipeline
<https://doi.org/10.12688/f1000research.16665.2>
<https://doi.org/10.1093/nargab/lqae031>
<https://doi.org/10.5281/zenodo.3476425>
* The nf-core framework
<https://doi.org/10.1038/s41587-020-0439-x>
* Software dependencies
<https://github.com/nf-core/sarek/blob/master/CITATIONS.md>
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[9d/41a215] NFC…n.exome.b37.interval_list) | 1 of 1, cached: 1
executor > slurm (2954)
[9d/41a215] NFC…n.exome.b37.interval_list) | 1 of 1, cached: 1
[e9/ea5584] NFC…ED (Broad.human.exome.b37) | 1 of 1, cached: 1 ✔
[25/95a17f] NFC…PLIT (6_43498426-43498562) | 82429 of 82429, cached: 82429
[ed/f6ad85] NFC…ED (Broad.human.exome.b37) | 1 of 1, cached: 1 ✔
[- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR -
[- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ -
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[- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP -
[- ] NFC…:SAMTOOLS_VIEW_UNMAP_UNMAP -
[- ] NFC…UT:SAMTOOLS_VIEW_UNMAP_MAP -
[- ] NFC…UT:SAMTOOLS_VIEW_MAP_UNMAP -
[- ] NFC…INPUT:SAMTOOLS_MERGE_UNMAP -
[- ] NFC…_INPUT:COLLATE_FASTQ_UNMAP -
[- ] NFC…TQ_INPUT:COLLATE_FASTQ_MAP -
[- ] NFC…VERT_FASTQ_INPUT:CAT_FASTQ -
[5f/6af175] NFC…EK:FASTQC (SRR18056757-l1) | 8 of 8, cached: 8 ✔
[f4/d9f6a8] NFC…ATK:FASTP (SRR18056757-l1) | 8 of 8, cached: 8 ✔
[b2/f9f3d6] NFC…:BWAMEM1_MEM (SRR18056757) | 96 of 96, cached: 96 ✔
[- ] NFC…TK:FASTQ_ALIGN:BWAMEM2_MEM -
[- ] NFC…:FASTQ_ALIGN:DRAGMAP_ALIGN -
[c5/4f63ab] NFC…RKDUPLICATES (SRR18056757) | 8 of 8, cached: 8 ✔
[5d/c474b9] NFC…MTOOLS_STATS (SRR18056757) | 8 of 8, cached: 8 ✔
[36/bb7980] NFC…OLS:MOSDEPTH (SRR18056757) | 8 of 8, cached: 8 ✔
[3c/409a86] NFC…:CRAM_TO_BAM (SRR18056757) | 8 of 8, cached: 8 ✔
[ac/d4e8ea] NFC…RECALIBRATOR (SRR18056733) | 6305 of 172646, cached: 3360
Plus 17 more processes waiting for tasks…
cat /home/iaperez/.nextflow/configs/new.cluster1.config
process {
executor = 'slurm'
queue = 'main' // force main partition
queueSize = 200
pollInterval = '1 min'
dumpInterval = '5 min'
queueStatInterval = '2 min'
exitReadTimeout = '60 sec'
killBatchSize = 16
submitRateLimit = '1 sec'
perJobMemLimit = 'slurm'
jobName = 'nf-NFCORE'
// Default resources for lightweight processes
cpus = 8
memory = '24 GB'
time = '12h' // default 8h to avoid SLURM timeouts
}
// Override for heavy alignment steps (BWA-MEM)
process {
withName: '.*BWAMEM1_MEM.*' {
cpus = 12
memory = '32 GB'
time = '23h' // under 24h for main partition
}
}
// Override for GATK BaseRecalibrator (prevent OOM)
process {
withName: '.*GATK4_BASERECALIBRATOR.*' {
cpus = 6
memory = '16 GB' // previously 3GB too low
time = '12h'
}
}
singularity {
enabled = true
autoMounts = true // keep mounts
// runOptions removed to prevent --cleanenv killing env vars
}
env {
NXF_OPTS = '-Xms2g -Xmx20g'
// force singularity to use cluster scratch to prevent extraction OOM
SINGULARITY_TMPDIR = '/storage/scratch01/groups/ce/BLCA_Germline/tmp'
SINGULARITY_CACHEDIR = '/storage/scratch01/groups/ce/BLCA_Germline/singularity_cache'
}