Hello, Please go at the end of the message to find directly the solution. I tried to run sarek with UMI inside reads (raw data), I am not able to have bam files and there is no error. Then I tried to move the UMI in the header, same results: no bam and no error. So, if it is only a problem linked to UMI, let's try to run sarek without UMI at all and by trimming it. However, it seems the problem is outside UMI scope (at least in my case, do not know for @George Seed case), because I still do not have an output bam file and neither an error message. Here what I launch:

export JAVA_CMD=/usr/lib/jvm/java-25-openjdk-amd64/bin/java
export JAVA_HOME=/usr/lib/jvm/java-25-openjdk-amd64
export NXF_OPTS='-Xmx20g -XX:-ExitOnOutOfMemoryError'

rm -rf work/ 2026-02-04_SRP_NGShem/*

nextflow run nf-core/sarek -profile singularity --input /mnt/HDD2/sarek_inhouse_hg19/samplesheet_mapping_NGShem.csv --outdir /mnt/HDD2/sarek_inhouse_hg19/2026-02-04_SRP_NGShem/ -r 3.8.1 -with-report -with-trace -with-timeline -with-dag -params-file /mnt/HDD2/sarek_inhouse_hg19/ipa_params_noUMI.json

The sample sheet:

cat /mnt/HDD2/sarek_inhouse_hg19/samplesheet_mapping_NGShem.csv
patient,sex,status,sample,lane,fastq_1,fastq_2
C2508328-star,NA,1,C2508328-star,L1,/mnt/SHARE_NGSDATA/IPA_NHE/260204_VH01811_146_AAHJLJCM5/Analysis/1/Data/fastq/C2508328-star_S1_R1_001.fastq.gz,/mnt/SHARE_NGSDATA/IPA_NHE/260204_VH01811_146_AAHJLJCM5/Analysis/1/Data/fastq/C2508328-star_S1_R2_001.fastq.gz

The new params file:

cat /mnt/HDD2/sarek_inhouse_hg19/ipa_params_noUMI.json
{
    "igenomes_ignore":           true,
    "genome":                    "GATK.GRCh37",
    "steps":                     "mapping",
    "wes":                       true,
    "trim_fastq":                true,
    "clip_r1":                   7,
    "clip_r2":                   7,
    "save_trimmed":              true,
    "dbsnp":                     "/mnt/HDD2/sarek_inhouse_hg19/bgzip_input/dbsnp_138.b37.vcf.gz",
    "intervals":                 "/mnt/ARC/IPA/CBIOMOL_ARCH/MISEQ_bioinfo/Heme.panel/Annotation/HemePanel.padded.Nochr.v4.bed",
    "known_indels":              "/mnt/HDD2/sarek_inhouse_hg19/bgzip_input/1000G_phase1.indels.b37.vcf.gz",
    "known_snps":                "/mnt/HDD2/sarek_inhouse_hg19/bgzip_input/1000G_phase1.snps.high_confidence.b37.vcf.gz",
    "pon":                       "/mnt/HDD2/sarek_inhouse_hg19/bgzip_input/MuTect2_PON.vcf.gz",
    "max_cpus":                  90,
    "max_memory":                "120 GB"
}

And the execution trace:

cut -f2,4,5 2026-02-04_SRP_NGShem/pipeline_info/execution_trace_2026-*.txt
hash    name    status
da/3edd83       NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (HemePanel.padded.Nochr.v4.bed)     COMPLETED
6b/50e398       NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (HemePanel.padded.Nochr.v4)   COMPLETED
56/1918fd       NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS (1000G_phase1.indels.b37.vcf)    COMPLETED
1b/de4a86       NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (1_1718760-1718886)      COMPLETED
64/37dfeb       NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS (1000G_phase1.snps.high_confidence.b37.vcf)        COMPLETED
2b/d92b32       NFCORE_SAREK:PREPARE_GENOME:TABIX_DBSNP (dbsnp_138.b37.vcf)     COMPLETED
47/df18b4       NFCORE_SAREK:sarek:FASTQ_PREPROCESS_GATK:FASTP (C2508328-star-L1)       COMPLETED
ad/84da0e       NFCORE_SAREK:sarek:FASTQC (C2508328-star-L1)    COMPLETED
94/3ef17b       NFCORE_SAREK:sarek:MULTIQC      COMPLETED

There is an correct output of trimmed fastq:

zcat 2026-02-04_SRP_NGShem/preprocessing/fastp/C2508328-star/0001.C2508328-star-L1_1.fastp.fastq.gz | head -n 2

@VH01811146AAHJLJCM511101184591000 1N0:CGTTCTCTTG+CCACTTGGTG ATGGTGAGCTCTTGGAGGGCGGGGCACAGAGGCCTGCCCCCCTT

zcat /mnt/SHARE_NGSDATA/IPA_NHE/260204_VH01811_146_AAHJLJCM5/Analysis/1/Data/fastq/C2508328-star_S1_R1_001.fastq.gz | grep -P -A 1 -m 1 "^@VH01811:146:AAHJLJCM5:1:1101:18459:1000"

@VH01811146AAHJLJCM511101184591000 1N0:CGTTCTCTTG+CCACTTGGTG GTGAGAT*ATGGTGAGCTCTTGGAGGGCGGGGCACAGAGGCCTGCCCCCCTT* But still no output bam files:

find work/ 2026-02-04_SRP_NGShem/ -name "*.bam" -o -name "*.cram" -o -name "*sam"

However I finally manage to find the problem: in the sample sheet there are probably two parameters that cannot be together:

"igenomes_ignore":           true,
    "genome":                    "GATK.GRCh37",

I removed igenomes_ignore and bwa mem is running! Maybe sarek could print a message like —bwa reference_genome is needed if igenomes_ignore is set to true? Best, Vimel

oh