(base) [ash022@login-4.SAGA /cluster/projects/nn9036k/precFDA]$ ./nextflow run nf-core/sarek -profile test,singularity
N E X T F L O W ~ version 22.04.4
Pulling nf-core/sarek ...
downloaded from https://github.com/nf-core/sarek.git
Launching `https://github.com/nf-core/sarek` [magical_nightingale] DSL1 - revision: e8f56e5bbb [master]
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| \| | \__, \__/ | \ |___ \`-._,-`-,
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/ |\`-_ \ __ __ ___
| | \ `-| |__` /\ |__) |__ |__/
\ | \ / .__| /¯¯\ | \ |___ | \
`|____\´
nf-core/sarek v2.7.2
------------------------------------------------------
Core Nextflow options
revision : master
runName : magical_nightingale
containerEngine : singularity
container : nfcore/sarek:2.7.2
launchDir : /cluster/projects/nn9036k/precFDA
workDir : /cluster/projects/nn9036k/precFDA/work
projectDir : /cluster/home/ash022/.nextflow/assets/nf-core/sarek
userName : ash022
profile : test,singularity
configFiles : /cluster/home/ash022/.nextflow/assets/nf-core/sarek/nextflow.config
Input/output options
input : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/tsv/tiny-manta-https.tsv
Main options
tools : null
skip_qc : null
Trim/split FASTQ
clip_r1 : 0
clip_r2 : 0
three_prime_clip_r1 : 0
three_prime_clip_r2 : 0
trim_nextseq : 0
Preprocessing
markdup_java_options : "-Xms4000m -Xmx7g"
Variant Calling
ascat_ploidy : null
ascat_purity : null
cf_contamination : null
cf_ploidy : 2
read_structure1 : null
read_structure2 : null
Annotation
annotate_tools : null
cadd_indels : false
cadd_indels_tbi : false
cadd_wg_snvs : false
cadd_wg_snvs_tbi : false
snpeff_cache : null
vep_cache : null
Reference genome options
genome : smallGRCh37
dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz
fasta : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta
intervals : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/small.intervals
known_indels : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.smal l.vcf.gz
snpeff_db : WBcel235.86
species : caenorhabditis_elegans
vep_cache_version : 99
igenomes_base : s3://ngi-igenomes/igenomes/
genomes_base : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference
igenomes_ignore : true
Generic options
max_multiqc_email_size : 25 MB
sequencing_center : null
Max job request options
single_cpu_mem : 7 GB
max_cpus : 2
max_memory : 6 GB
max_time : 2d
Institutional config options
config_profile_name : Test profile
config_profile_description: Minimal test dataset to check pipeline function
------------------------------------------------------
Only displaying parameters that differ from defaults.
------------------------------------------------------
Pipeline Release : master
Run Name : magical_nightingale
Max Resources : 6 GB memory, 2 cpus, 2d time per job
Container : singularity - nfcore/sarek:2.7.2
Output dir : ./results
Launch dir : /cluster/projects/nn9036k/precFDA
Working dir : /cluster/projects/nn9036k/precFDA/work
Script dir : /cluster/home/ash022/.nextflow/assets/nf-core/sarek
User : ash022
Input : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/tsv/tiny-manta-https.tsv
Step : mapping
Genome : smallGRCh37
Nucleotides/s : 1000
MarkDuplicates : Options
Java options : "-Xms4000m -Xmx7g"
GATK Spark : No
Save BAMs mapped : No
Skip MarkDuplicates: No
AWS iGenomes : Do not use
Save Reference : No
dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz
fasta reference : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta
intervals : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/small.intervals
known indels : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz
snpEff DB : WBcel235.86
species : caenorhabditis_elegans
VEP cache version : 99
Publish dir mode : copy
Config Profile : test,singularity
Config Description: Minimal test dataset to check pipeline function
Config Files : /cluster/home/ash022/.nextflow/assets/nf-core/sarek/nextflow.config
----------------------------------------------------
[- ] process > get_software_versions -
[- ] process > get_software_versions -
[- ] process > get_software_versions -
[- ] process > BuildBWAindexes -
[- ] process > BuildDict -
[- ] process > BuildFastaFai -
[- ] process > BuildDbsnpIndex -
[- ] process > get_software_versions -
[- ] process > BuildBWAindexes -
[- ] process > BuildDict -
[- ] process > BuildFastaFai -
[- ] process > BuildDbsnpIndex -
[- ] process > BuildGermlineResourceIndex -
[- ] process > BuildKnownIndelsIndex -
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[- ] process > CreateIntervalBeds -
[- ] process > FastQCFQ -
[- ] process > FastQCBAM -
[- ] process > TrimGalore -
[- ] process > UMIFastqToBAM -
[- ] process > UMIMapBamFile -
[- ] process > GroupReadsByUmi -
[- ] process > CallMolecularConsensusReads -
[- ] process > MapReads -
[- ] process > Sentieon_MapReads -
[- ] process > MergeBamMapped -
[- ] process > IndexBamMergedForSentieon -
[- ] process > IndexBamFile -
[- ] process > MarkDuplicates -
[- ] process > Sentieon_Dedup -
[- ] process > BaseRecalibrator -
[- ] process > GatherBQSRReports -
[- ] process > ApplyBQSR -
[- ] process > Sentieon_BQSR -
[- ] process > MergeBamRecal -
[- ] process > IndexBamRecal -
[- ] process > get_software_versions -
[- ] process > BuildBWAindexes -
[- ] process > BuildDict -
[- ] process > BuildFastaFai -
[- ] process > BuildDbsnpIndex -
[- ] process > BuildGermlineResourceIndex -
[- ] process > BuildKnownIndelsIndex -
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[- ] process > CreateIntervalBeds -
[- ] process > FastQCFQ -
[- ] process > FastQCBAM -
[- ] process > TrimGalore -
[- ] process > UMIFastqToBAM -
[- ] process > UMIMapBamFile -
[- ] process > GroupReadsByUmi -
[- ] process > CallMolecularConsensusReads -
[- ] process > MapReads -
[- ] process > Sentieon_MapReads -
[- ] process > MergeBamMapped -
[- ] process > IndexBamMergedForSentieon -
[- ] process > IndexBamFile -
[- ] process > MarkDuplicates -
[- ] process > Sentieon_Dedup -
[- ] process > BaseRecalibrator -
[- ] process > GatherBQSRReports -
[- ] process > ApplyBQSR -
[- ] process > Sentieon_BQSR -
[- ] process > MergeBamRecal -
[- ] process > IndexBamRecal -
[- ] process > SamtoolsStats -
[- ] process > BamQC -
[- ] process > get_software_versions -
[- ] process > BuildBWAindexes -
[- ] process > BuildDict -
[- ] process > BuildFastaFai -
[- ] process > BuildDbsnpIndex -
[- ] process > BuildGermlineResourceIndex -
[- ] process > BuildKnownIndelsIndex -
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[- ] process > CreateIntervalBeds -
[- ] process > FastQCFQ -
[- ] process > FastQCBAM -
[- ] process > TrimGalore -
[- ] process > UMIFastqToBAM -
[- ] process > UMIMapBamFile -
[- ] process > GroupReadsByUmi -
[- ] process > CallMolecularConsensusReads -
[- ] process > MapReads -
[- ] process > Sentieon_MapReads -
[- ] process > MergeBamMapped -
[- ] process > IndexBamMergedForSentieon -
[- ] process > IndexBamFile -
[- ] process > MarkDuplicates -
[- ] process > Sentieon_Dedup -
[- ] process > BaseRecalibrator -
[- ] process > GatherBQSRReports -
[- ] process > ApplyBQSR -
[- ] process > Sentieon_BQSR -
[- ] process > MergeBamRecal -
[- ] process > IndexBamRecal -
[- ] process > SamtoolsStats -
[- ] process > BamQC -
[- ] process > get_software_versions -
[- ] process > BuildBWAindexes -
[- ] process > BuildDict -
[- ] process > BuildFastaFai -
[- ] process > BuildDbsnpIndex -
[- ] process > BuildGermlineResourceIndex -
[- ] process > BuildKnownIndelsIndex -
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[- ] process > CreateIntervalBeds -
[- ] process > FastQCFQ -
[- ] process > FastQCBAM -
[- ] process > TrimGalore -
[- ] process > UMIFastqToBAM -
[- ] process > UMIMapBamFile -
[- ] process > GroupReadsByUmi -
[- ] process > CallMolecularConsensusReads -
[- ] process > MapReads -
[- ] process > Sentieon_MapReads -
[- ] process > MergeBamMapped -
[- ] process > IndexBamMergedForSentieon -
[- ] process > IndexBamFile -
[- ] process > MarkDuplicates -
[- ] process > Sentieon_Dedup -
[- ] process > BaseRecalibrator -
[- ] process > GatherBQSRReports -
[- ] process > ApplyBQSR -
[- ] process > Sentieon_BQSR -
[- ] process > MergeBamRecal -
[- ] process > IndexBamRecal -
[- ] process > SamtoolsStats -
[- ] process > BamQC -
[- ] process > get_software_versions [ 0%] 0 of 1
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[- ] process > BuildGermlineResourceIndex -
[- ] process > BuildKnownIndelsIndex -
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
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[- ] process > FastQCFQ [ 0%] 0 of 8
[- ] process > FastQCBAM -
[- ] process > TrimGalore -
[- ] process > UMIFastqToBAM -
[- ] process > UMIMapBamFile -
[- ] process > GroupReadsByUmi -
[- ] process > CallMolecularConsensusReads -
[- ] process > MapReads -
[- ] process > Sentieon_MapReads -
[- ] process > MergeBamMapped -
[- ] process > IndexBamMergedForSentieon -
[- ] process > IndexBamFile -
[- ] process > MarkDuplicates -
[- ] process > Sentieon_Dedup -
[- ] process > BaseRecalibrator -
[- ] process > GatherBQSRReports -
[- ] process > ApplyBQSR -
[- ] process > Sentieon_BQSR -
[- ] process > MergeBamRecal -
[- ] process > IndexBamRecal -
[- ] process > SamtoolsStats -
[- ] process > get_software_versions [ 0%] 0 of 1
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[- ] process > BuildKnownIndelsIndex [ 0%] 0 of 1
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[- ] process > CreateIntervalBeds [ 0%] 0 of 1
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[- ] process > FastQCBAM -
[- ] process > TrimGalore -
[- ] process > UMIFastqToBAM -
[- ] process > UMIMapBamFile -
[- ] process > GroupReadsByUmi -
[- ] process > CallMolecularConsensusReads -
[- ] process > MapReads -
[- ] process > Sentieon_MapReads -
[- ] process > MergeBamMapped -
[- ] process > IndexBamMergedForSentieon -
[- ] process > IndexBamFile -
[- ] process > MarkDuplicates -
[- ] process > Sentieon_Dedup -
[- ] process > BaseRecalibrator -
[- ] process > GatherBQSRReports -
[- ] process > ApplyBQSR -
[- ] process > Sentieon_BQSR -
[- ] process > MergeBamRecal -
[- ] process > IndexBamRecal -
[- ] process > SamtoolsStats -
executor > local (3)
[- ] process > get_software_versions [ 0%] 0 of 1
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[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
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[a1/53d746] process > FastQCFQ (1234-1234N_M7) [ 0%] 0 of 11
[- ] process > FastQCBAM -
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[- ] process > UMIFastqToBAM -
[- ] process > UMIMapBamFile -
[- ] process > GroupReadsByUmi -
[- ] process > CallMolecularConsensusReads -
[- ] process > MapReads -
[- ] process > Sentieon_MapReads -
[- ] process > MergeBamMapped -
[- ] process > IndexBamMergedForSentieon -
[- ] process > IndexBamFile -
[- ] process > MarkDuplicates -
[- ] process > Sentieon_Dedup -
[- ] process > BaseRecalibrator -
[- ] process > GatherBQSRReports -
[- ] process > ApplyBQSR -
[- ] process > Sentieon_BQSR -
[- ] process > MergeBamRecal -
executor > local (8)
[- ] process > get_software_versions [ 0%] 0 of 1
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[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
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[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
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[84/e197b3] process > FastQCFQ (1234-1234N_M5) [ 0%] 0 of 11
[- ] process > FastQCBAM -
[- ] process > TrimGalore -
[- ] process > UMIFastqToBAM -
[- ] process > UMIMapBamFile -
[- ] process > GroupReadsByUmi -
[- ] process > CallMolecularConsensusReads -
[- ] process > MapReads -
[- ] process > Sentieon_MapReads -
[- ] process > MergeBamMapped -
[- ] process > IndexBamMergedForSentieon -
[- ] process > IndexBamFile -
[- ] process > MarkDuplicates -
[- ] process > Sentieon_Dedup -
[- ] process > BaseRecalibrator -
[- ] process > GatherBQSRReports -
[- ] process > ApplyBQSR -
[- ] process > Sentieon_BQSR -
[- ] process > MergeBamRecal -
executor > local (11)
[- ] process > get_software_versions [ 0%] 0 of 1
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[- ] process > BuildFastaFai [ 0%] 0 of 1
[- ] process > BuildDbsnpIndex [ 0%] 0 of 1
[- ] process > BuildGermlineResourceIndex -
[- ] process > BuildKnownIndelsIndex [ 0%] 0 of 1
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [ 0%] 0 of 1
[05/d6c9c5] process > FastQCFQ (1234-9876T_M5) [ 0%] 0 of 11
[- ] process > FastQCBAM -
[- ] process > TrimGalore -
[- ] process > UMIFastqToBAM -
[- ] process > UMIMapBamFile -
[- ] process > GroupReadsByUmi -
[- ] process > CallMolecularConsensusReads -
[- ] process > MapReads -
[- ] process > Sentieon_MapReads -
[- ] process > MergeBamMapped -
[- ] process > IndexBamMergedForSentieon -
[- ] process > IndexBamFile -
[- ] process > MarkDuplicates -
[- ] process > Sentieon_Dedup -
[- ] process > BaseRecalibrator -
[- ] process > GatherBQSRReports -
[- ] process > ApplyBQSR -
[- ] process > Sentieon_BQSR -
[- ] process > MergeBamRecal -
executor > local (12)
[96/9b32b5] process > get_software_versions [ 0%] 0 of 1
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[- ] process > BuildFastaFai [ 0%] 0 of 1
[- ] process > BuildDbsnpIndex [ 0%] 0 of 1
[- ] process > BuildGermlineResourceIndex -
[- ] process > BuildKnownIndelsIndex [ 0%] 0 of 1
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [ 0%] 0 of 1
[05/d6c9c5] process > FastQCFQ (1234-9876T_M5) [ 0%] 0 of 11
[- ] process > FastQCBAM -
[- ] process > TrimGalore -
[- ] process > UMIFastqToBAM -
[- ] process > UMIMapBamFile -
[- ] process > GroupReadsByUmi -
[- ] process > CallMolecularConsensusReads -
[- ] process > MapReads -
[- ] process > Sentieon_MapReads -
[- ] process > MergeBamMapped -
[- ] process > IndexBamMergedForSentieon -
[- ] process > IndexBamFile -
[- ] process > MarkDuplicates -
[- ] process > Sentieon_Dedup -
[- ] process > BaseRecalibrator -
[- ] process > GatherBQSRReports -
[- ] process > ApplyBQSR -
[- ] process > Sentieon_BQSR -
[- ] process > MergeBamRecal -
executor > local (13)
[96/9b32b5] process > get_software_versions [ 0%] 0 of 1
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[e9/a76cc8] process > BuildFastaFai (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[- ] process > BuildDbsnpIndex [ 0%] 0 of 1
[- ] process > BuildGermlineResourceIndex -
[- ] process > BuildKnownIndelsIndex [ 0%] 0 of 1
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [ 0%] 0 of 1
[05/d6c9c5] process > FastQCFQ (1234-9876T_M5) [ 0%] 0 of 11
[- ] process > FastQCBAM -
[- ] process > TrimGalore -
[- ] process > UMIFastqToBAM -
[- ] process > UMIMapBamFile -
[- ] process > GroupReadsByUmi -
[- ] process > CallMolecularConsensusReads -
[- ] process > MapReads -
[- ] process > Sentieon_MapReads -
[- ] process > MergeBamMapped -
[- ] process > IndexBamMergedForSentieon -
[- ] process > IndexBamFile -
[- ] process > MarkDuplicates -
[- ] process > Sentieon_Dedup -
[- ] process > BaseRecalibrator -
[- ] process > GatherBQSRReports -
[- ] process > ApplyBQSR -
[- ] process > Sentieon_BQSR -
[- ] process > MergeBamRecal -
executor > local (19)
[96/9b32b5] process > get_software_versions [ 0%] 0 of 1
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[e9/a76cc8] process > BuildFastaFai (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[a9/2450aa] process > BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz) [ 0%] 0 of 1
[- ] process > BuildGermlineResourceIndex -
[9a/8dfbd0] process > BuildKnownIndelsIndex (Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz) [ 0%] 0 of 1
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [ 0%] 0 of 1
[78/da8cb3] process > FastQCFQ (1234-9876T_M3) [ 0%] 0 of 11
[- ] process > FastQCBAM -
[- ] process > TrimGalore -
[- ] process > UMIFastqToBAM -
[- ] process > UMIMapBamFile -
[- ] process > GroupReadsByUmi -
[- ] process > CallMolecularConsensusReads -
[- ] process > MapReads -
[- ] process > Sentieon_MapReads -
[- ] process > MergeBamMapped -
[- ] process > IndexBamMergedForSentieon -
[- ] process > IndexBamFile -
[- ] process > MarkDuplicates -
[- ] process > Sentieon_Dedup -
[- ] process > BaseRecalibrator -
[- ] process > GatherBQSRReports -
[- ] process > ApplyBQSR -
[- ] process > Sentieon_BQSR -
[- ] process > MergeBamRecal -
executor > local (19)
[96/9b32b5] process > get_software_versions [ 0%] 0 of 1
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[e9/a76cc8] process > BuildFastaFai (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[a9/2450aa] process > BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz) [ 0%] 0 of 1
[- ] process > BuildGermlineResourceIndex -
[9a/8dfbd0] process > BuildKnownIndelsIndex (Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz) [ 0%] 0 of 1
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [ 0%] 0 of 1
[78/da8cb3] process > FastQCFQ (1234-9876T_M3) [ 0%] 0 of 11
...
executor > local (19)
[96/9b32b5] process > get_software_versions [ 0%] 0 of 1
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[e9/a76cc8] process > BuildFastaFai (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[a9/2450aa] process > BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz) [ 0%] 0 of 1
[- ] process > BuildGermlineResourceIndex -
[9a/8dfbd0] process > BuildKnownIndelsIndex (Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz) [ 0%] 0 of 1
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [ 0%] 0 of 1
[78/da8cb3] process > FastQCFQ (1234-9876T_M3) [ 0%] 0 of 11
...
executor > local (19)
[96/9b32b5] process > get_software_versions [ 0%] 0 of 1
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [ 0%] 0 of 1
[e9/a76cc8] process > BuildFastaFai (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[a9/2450aa] process > BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildGermlineResourceIndex -
[9a/8dfbd0] process > BuildKnownIndelsIndex (Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [100%] 1 of 1 ✔
[78/da8cb3] process > FastQCFQ (1234-9876T_M3) [ 0%] 0 of 11
...
executor > local (19)
[96/9b32b5] process > get_software_versions [ 0%] 0 of 1
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[e9/a76cc8] process > BuildFastaFai (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[a9/2450aa] process > BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildGermlineResourceIndex -
[9a/8dfbd0] process > BuildKnownIndelsIndex (Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [100%] 1 of 1 ✔
[78/da8cb3] process > FastQCFQ (1234-9876T_M3) [ 0%] 0 of 11
...
executor > local (19)
[96/9b32b5] process > get_software_versions [ 0%] 0 of 1
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[e9/a76cc8] process > BuildFastaFai (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[a9/2450aa] process > BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildGermlineResourceIndex -
[9a/8dfbd0] process > BuildKnownIndelsIndex (Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [100%] 1 of 1 ✔
[94/6300a4] process > FastQCFQ (1234-1234N_M6) [ 45%] 5 of 11
...
executor > local (19)
[96/9b32b5] process > get_software_versions [ 0%] 0 of 1
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[e9/a76cc8] process > BuildFastaFai (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[a9/2450aa] process > BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildGermlineResourceIndex -
[9a/8dfbd0] process > BuildKnownIndelsIndex (Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [100%] 1 of 1 ✔
[fe/52791d] process > FastQCFQ (1234-1234N_M4) [ 54%] 6 of 11
...
executor > local (19)
[96/9b32b5] process > get_software_versions [ 0%] 0 of 1
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[e9/a76cc8] process > BuildFastaFai (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[a9/2450aa] process > BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildGermlineResourceIndex -
[9a/8dfbd0] process > BuildKnownIndelsIndex (Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [100%] 1 of 1 ✔
[0c/5070e9] process > FastQCFQ (1234-9876T_M1) [ 81%] 9 of 11
...
executor > local (19)
[96/9b32b5] process > get_software_versions [ 0%] 0 of 1
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[e9/a76cc8] process > BuildFastaFai (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[a9/2450aa] process > BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildGermlineResourceIndex -
[9a/8dfbd0] process > BuildKnownIndelsIndex (Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [100%] 1 of 1 ✔
[3b/313b53] process > FastQCFQ (1234-9876T_M2) [100%] 11 of 11 ✔
...
executor > local (19)
[96/9b32b5] process > get_software_versions [100%] 1 of 1, failed: 1 ✘
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[e9/a76cc8] process > BuildFastaFai (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[a9/2450aa] process > BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildGermlineResourceIndex -
[9a/8dfbd0] process > BuildKnownIndelsIndex (Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [100%] 1 of 1 ✔
[3b/313b53] process > FastQCFQ (1234-9876T_M2) [100%] 11 of 11 ✔
...
executor > local (19)
[96/9b32b5] process > get_software_versions [100%] 1 of 1, failed: 1 ✘
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[e9/a76cc8] process > BuildFastaFai (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[a9/2450aa] process > BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildGermlineResourceIndex -
[9a/8dfbd0] process > BuildKnownIndelsIndex (Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [100%] 1 of 1 ✔
[3b/313b53] process > FastQCFQ (1234-9876T_M2) [100%] 11 of 11 ✔
...
executor > local (19)
[96/9b32b5] process > get_software_versions [100%] 1 of 1, failed: 1 ✘
[8d/b0f454] process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[f4/1ba4bf] process > BuildDict (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[e9/a76cc8] process > BuildFastaFai (human_g1k_v37_decoy.small.fasta) [100%] 1 of 1 ✔
[a9/2450aa] process > BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildGermlineResourceIndex -
[9a/8dfbd0] process > BuildKnownIndelsIndex (Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz) [100%] 1 of 1 ✔
[- ] process > BuildPonIndex -
[- ] process > BuildIntervals -
[4a/29ce35] process > CreateIntervalBeds (small.intervals) [100%] 1 of 1 ✔
[3b/313b53] process > FastQCFQ (1234-9876T_M2) [100%] 11 of 11 ✔
...
[7d/6054e0] process > Output_documentation [100%] 1 of 1, failed: 1 ✘
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/sarek] Pipeline completed with errors-
Error executing process > 'Output_documentation'
Caused by:
Process `Output_documentation` terminated with an error exit status (127)
Command executed:
markdown_to_html.py output.md -o results_description.html
Command exit status:
127
Command output:
(empty)
Command error:
/usr/bin/env: ‘python\r’: No such file or directory
Work dir:
/cluster/projects/nn9036k/precFDA/work/7d/6054e04beeca8c1083c627bc7068df
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
Description of the bug
Checking the workflow using test command
Steps to reproduce