ybdong919
commented
2 months ago Command used:
nextflow run ./sarek -profile singularity --input samplesheet.csv --outdir ./Candida --tools 'freebayes,snpeff' --genome null --igenomes_ignore --fasta ./ref/hs37d5.fa --skip_tools baserecalibrator --snpeff_cache ...../
Terminal output: N E X T F L O W ~ version 24.04.4
Launching ./sarek/main.nf [trusting_dijkstra] DSL2 - revision: e3d6110e17
WARN: Access to undefined parameter monochromeLogs -- Initialise it to a default value eg. params.monochromeLogs = some_value
,--./,-.
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nf-core/sarek v3.4.4
Core Nextflow options runName : trusting_dijkstra containerEngine : singularity launchDir : /blue/bphl-florida/dongyibo/nf-core/sarek workDir : /blue/bphl-florida/dongyibo/nf-core/sarek/work projectDir : /blue/bphl-florida/dongyibo/nf-core/sarek/sarek userName : dongyibo profile : singularity configFiles :
Input/output options input : samplesheet.csv outdir : ./Candida
Main options tools : freebayes,snpeff skip_tools : baserecalibrator .... .... .... -- Check '.nextflow.log' file for details
executor > local (83) [c9/a8d30f] NFC…:BWAMEM1_INDEX (hs37d5.fa) | 1 of 1 ✔ [- ] NFC…EPARE_GENOME:BWAMEM2_INDEX - [- ] NFC…E_GENOME:DRAGMAP_HASHTABLE - [d3/9b5dfb] NFC…ENCEDICTIONARY (hs37d5.fa) | 1 of 1 ✔ [- ] NFC…E_GENOME:MSISENSORPRO_SCAN - [bb/9ae97e] NFC…SAMTOOLS_FAIDX (hs37d5.fa) | 1 of 1 ✔ [- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS - [- ] NFC…PREPARE_GENOME:TABIX_DBSNP - [- ] NFC…ME:TABIX_GERMLINE_RESOURCE - [- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS - [- ] NFC…_GENOME:TABIX_KNOWN_INDELS - [- ] NFC…K:PREPARE_GENOME:TABIX_PON - [ad/2b40fb] NFC…S:BUILD_INTERVALS (hs37d5) | 1 of 1 ✔ [50/b5d9e2] NFC…INTERVALS_BED (hs37d5.bed) | 1 of 1 ✔ [54/624f89] NFC…RVAL_SPLIT (4_1-191154276) | 18 of 18 ✔ [ff/c3922b] NFC…INTERVAL_COMBINED (hs37d5) | 1 of 1 ✔ [- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR - [- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ - [- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ - [- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP - [6e/0e407a] NFC…REK:SAREK:FASTQC (S1-L002) | 1 of 1 ✔ [7e/5b706c] NFC…AREK:SAREK:FASTP (S1-L002) | 1 of 1 ✔ [a4/ad2737] NFC…_SENTIEON:BWAMEM1_MEM (S1) | 12 of 12 ✔ [b4/903f14] NFC…:GATK4_MARKDUPLICATES (S1) | 1 of 1 ✔ [fe/613a18] NFC…MTOOLS:SAMTOOLS_STATS (S1) | 1 of 1 ✔ [67/641dc4] NFC…PTH_SAMTOOLS:MOSDEPTH (S1) | 1 of 1 ✔ [f8/cd6441] NFC…G_FREEBAYES:FREEBAYES (S1) | 18 of 18 ✔ [7a/9bb374] NFC…EEBAYES:BCFTOOLS_SORT (S1) | 18 of 18 ✔ [4f/fc66d0] NFC…BAYES:MERGE_FREEBAYES (S1) | 1 of 1 ✔ [42/fec85a] NFC…FTOOLS:BCFTOOLS_STATS (S1) | 1 of 1 ✔ [dd/de5de9] NFC…S:VCFTOOLS_TSTV_COUNT (S1) | 1 of 1 ✔ [b6/af9e8f] NFC…LS:VCFTOOLS_TSTV_QUAL (S1) | 1 of 1 ✔ [81/ec6c50] NFC…OOLS:VCFTOOLS_SUMMARY (S1) | 1 of 1 ✔ [f1/aa0a68] NFC…_SNPEFF:SNPEFF_SNPEFF (S1) | 1 of 1, failed: 1 ✘ Plus 24 more processes waiting for tasks… Pulling Singularity image https://depot.galaxyproject.org/singularity/snpeff:5.1--hdfd78af_2 [cache /blue/bphl-florida/dongyibo/nf-core/sarek/work/singularity/depot.galaxyproject.org-singularity-snpeff-5.1--hdfd78af_2.img] Pulling Singularity image https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4 [cache /blue/bphl-florida/dongyibo/nf-core/sarek/work/singularity/depot.galaxyproject.org-singularity-vcftools-0.1.16--he513fc3_4.img] Execution cancelled -- Finishing pending tasks before exit ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (S1)'
Caused by:
Process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (S1) terminated with an error exit status (255)
Command executed:
snpEff \ -Xmx29491M \ null.null \ -nodownload -canon -v \ -csvStats S1.freebayes_snpEff.csv \ -dataDir ${PWD}/candida_auris.5 \ S1.freebayes.vcf.gz \
S1.freebayes_snpEff.ann.vcf
cat <<-END_VERSIONS > versions.yml "NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF": snpeff: $(echo $(snpEff -version 2>&1) | cut -f 2 -d ' ') END_VERSIONS
Command exit status: 255
Command output: (empty)
Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
00:00:00 SnpEff version SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani
00:00:00 Command: 'ann'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'null.null'
00:00:00 Reading config file: snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.1-2/snpEff.config
java.lang.RuntimeException: Property: 'null.null.genome' not found
at org.snpeff.interval.Genome.
Work dir: /blue/bphl-florida/dongyibo/nf-core/sarek/work/f1/aa0a689fee1dc19e95facea7a517d5
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 ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details
executor > local (83) [c9/a8d30f] NFC…:BWAMEM1_INDEX (hs37d5.fa) | 1 of 1 ✔ [- ] NFC…EPARE_GENOME:BWAMEM2_INDEX - [- ] NFC…E_GENOME:DRAGMAP_HASHTABLE - [d3/9b5dfb] NFC…ENCEDICTIONARY (hs37d5.fa) | 1 of 1 ✔ [- ] NFC…E_GENOME:MSISENSORPRO_SCAN - [bb/9ae97e] NFC…SAMTOOLS_FAIDX (hs37d5.fa) | 1 of 1 ✔ [- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS - [- ] NFC…PREPARE_GENOME:TABIX_DBSNP - [- ] NFC…ME:TABIX_GERMLINE_RESOURCE - [- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS - [- ] NFC…_GENOME:TABIX_KNOWN_INDELS - [- ] NFC…K:PREPARE_GENOME:TABIX_PON - [ad/2b40fb] NFC…S:BUILD_INTERVALS (hs37d5) | 1 of 1 ✔ [50/b5d9e2] NFC…INTERVALS_BED (hs37d5.bed) | 1 of 1 ✔ [54/624f89] NFC…RVAL_SPLIT (4_1-191154276) | 18 of 18 ✔ [ff/c3922b] NFC…INTERVAL_COMBINED (hs37d5) | 1 of 1 ✔ [- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR - [- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ - [- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ - [- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP - [6e/0e407a] NFC…REK:SAREK:FASTQC (S1-L002) | 1 of 1 ✔ [7e/5b706c] NFC…AREK:SAREK:FASTP (S1-L002) | 1 of 1 ✔ [a4/ad2737] NFC…_SENTIEON:BWAMEM1_MEM (S1) | 12 of 12 ✔ [b4/903f14] NFC…:GATK4_MARKDUPLICATES (S1) | 1 of 1 ✔ [fe/613a18] NFC…MTOOLS:SAMTOOLS_STATS (S1) | 1 of 1 ✔ [67/641dc4] NFC…PTH_SAMTOOLS:MOSDEPTH (S1) | 1 of 1 ✔ [f8/cd6441] NFC…G_FREEBAYES:FREEBAYES (S1) | 18 of 18 ✔ [7a/9bb374] NFC…EEBAYES:BCFTOOLS_SORT (S1) | 18 of 18 ✔ [4f/fc66d0] NFC…BAYES:MERGE_FREEBAYES (S1) | 1 of 1 ✔ [42/fec85a] NFC…FTOOLS:BCFTOOLS_STATS (S1) | 1 of 1 ✔ [dd/de5de9] NFC…S:VCFTOOLS_TSTV_COUNT (S1) | 1 of 1 ✔ [b6/af9e8f] NFC…LS:VCFTOOLS_TSTV_QUAL (S1) | 1 of 1 ✔ [81/ec6c50] NFC…OOLS:VCFTOOLS_SUMMARY (S1) | 1 of 1 ✔ [f1/aa0a68] NFC…_SNPEFF:SNPEFF_SNPEFF (S1) | 1 of 1, failed: 1 ✘ Plus 24 more processes waiting for tasks… Pulling Singularity image https://depot.galaxyproject.org/singularity/snpeff:5.1--hdfd78af_2 [cache /blue/bphl-florida/dongyibo/nf-core/sarek/work/singularity/depot.galaxyproject.org-singularity-snpeff-5.1--hdfd78af_2.img] Pulling Singularity image https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4 [cache /blue/bphl-florida/dongyibo/nf-core/sarek/work/singularity/depot.galaxyproject.org-singularity-vcftools-0.1.16--he513fc3_4.img] Execution cancelled -- Finishing pending tasks before exit -[nf-core/sarek] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (S1)'
Caused by:
Process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (S1) terminated with an error exit status (255)
Command executed:
snpEff \ -Xmx29491M \ null.null \ -nodownload -canon -v \ -csvStats S1.freebayes_snpEff.csv \ -dataDir ${PWD}/candida_auris.5 \ S1.freebayes.vcf.gz \
S1.freebayes_snpEff.ann.vcf
cat <<-END_VERSIONS > versions.yml "NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF": snpeff: $(echo $(snpEff -version 2>&1) | cut -f 2 -d ' ') END_VERSIONS
Command exit status: 255
Command output: (empty)
Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
00:00:00 SnpEff version SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani
00:00:00 Command: 'ann'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'null.null'
00:00:00 Reading config file: snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.1-2/snpEff.config
java.lang.RuntimeException: Property: 'null.null.genome' not found
at org.snpeff.interval.Genome.
Work dir: /blue/bphl-florida/dongyibo/nf-core/sarek/work/f1/aa0a689fee1dc19e95facea7a517d5
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 ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details
executor > local (83) [c9/a8d30f] NFC…:BWAMEM1_INDEX (hs37d5.fa) | 1 of 1 ✔ [- ] NFC…EPARE_GENOME:BWAMEM2_INDEX - [- ] NFC…E_GENOME:DRAGMAP_HASHTABLE - [d3/9b5dfb] NFC…ENCEDICTIONARY (hs37d5.fa) | 1 of 1 ✔ [- ] NFC…E_GENOME:MSISENSORPRO_SCAN - [bb/9ae97e] NFC…SAMTOOLS_FAIDX (hs37d5.fa) | 1 of 1 ✔ [- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS - [- ] NFC…PREPARE_GENOME:TABIX_DBSNP - [- ] NFC…ME:TABIX_GERMLINE_RESOURCE - [- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS - [- ] NFC…_GENOME:TABIX_KNOWN_INDELS - [- ] NFC…K:PREPARE_GENOME:TABIX_PON - [ad/2b40fb] NFC…S:BUILD_INTERVALS (hs37d5) | 1 of 1 ✔ [50/b5d9e2] NFC…INTERVALS_BED (hs37d5.bed) | 1 of 1 ✔ [54/624f89] NFC…RVAL_SPLIT (4_1-191154276) | 18 of 18 ✔ [ff/c3922b] NFC…INTERVAL_COMBINED (hs37d5) | 1 of 1 ✔ [- ] NFC…RING_DECOMPRESS_TO_FQ_PAIR - [- ] NFC…SPRING_DECOMPRESS_TO_R1_FQ - [- ] NFC…SPRING_DECOMPRESS_TO_R2_FQ - [- ] NFC…NPUT:SAMTOOLS_VIEW_MAP_MAP - [6e/0e407a] NFC…REK:SAREK:FASTQC (S1-L002) | 1 of 1 ✔ [7e/5b706c] NFC…AREK:SAREK:FASTP (S1-L002) | 1 of 1 ✔ [a4/ad2737] NFC…_SENTIEON:BWAMEM1_MEM (S1) | 12 of 12 ✔ [b4/903f14] NFC…:GATK4_MARKDUPLICATES (S1) | 1 of 1 ✔ [fe/613a18] NFC…MTOOLS:SAMTOOLS_STATS (S1) | 1 of 1 ✔ [67/641dc4] NFC…PTH_SAMTOOLS:MOSDEPTH (S1) | 1 of 1 ✔ [f8/cd6441] NFC…G_FREEBAYES:FREEBAYES (S1) | 18 of 18 ✔ [7a/9bb374] NFC…EEBAYES:BCFTOOLS_SORT (S1) | 18 of 18 ✔ [4f/fc66d0] NFC…BAYES:MERGE_FREEBAYES (S1) | 1 of 1 ✔ [42/fec85a] NFC…FTOOLS:BCFTOOLS_STATS (S1) | 1 of 1 ✔ [dd/de5de9] NFC…S:VCFTOOLS_TSTV_COUNT (S1) | 1 of 1 ✔ [b6/af9e8f] NFC…LS:VCFTOOLS_TSTV_QUAL (S1) | 1 of 1 ✔ [81/ec6c50] NFC…OOLS:VCFTOOLS_SUMMARY (S1) | 1 of 1 ✔ [f1/aa0a68] NFC…_SNPEFF:SNPEFF_SNPEFF (S1) | 1 of 1, failed: 1 ✘ Plus 24 more processes waiting for tasks… Pulling Singularity image https://depot.galaxyproject.org/singularity/snpeff:5.1--hdfd78af_2 [cache /blue/bphl-florida/dongyibo/nf-core/sarek/work/singularity/depot.galaxyproject.org-singularity-snpeff-5.1--hdfd78af_2.img] Pulling Singularity image https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4 [cache /blue/bphl-florida/dongyibo/nf-core/sarek/work/singularity/depot.galaxyproject.org-singularity-vcftools-0.1.16--he513fc3_4.img] Execution cancelled -- Finishing pending tasks before exit -[nf-core/sarek] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (S1)'
Caused by:
Process NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (S1) terminated with an error exit status (255)
Command executed:
snpEff \ -Xmx29491M \ null.null \ -nodownload -canon -v \ -csvStats S1.freebayes_snpEff.csv \ -dataDir ${PWD}/candida_auris.5 \ S1.freebayes.vcf.gz \
S1.freebayes_snpEff.ann.vcf
cat <<-END_VERSIONS > versions.yml "NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF": snpeff: $(echo $(snpEff -version 2>&1) | cut -f 2 -d ' ') END_VERSIONS
Command exit status: 255
Command output: (empty)
Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
00:00:00 SnpEff version SnpEff 5.1d (build 2022-04-19 15:49), by Pablo Cingolani
00:00:00 Command: 'ann'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'null.null'
00:00:00 Reading config file: snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.1-2/snpEff.config
java.lang.RuntimeException: Property: 'null.null.genome' not found
at org.snpeff.interval.Genome.
Work dir: /blue/bphl-florida/dongyibo/nf-core/sarek/work/f1/aa0a689fee1dc19e95facea7a517d5
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 ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details
asp8200
maxulysse
Description of the bug
How can I use a custom snpeff reference database, such as candida.auris, in Sarek. This snpeff reference did not included in Sarek. I tried --snpeff_cache, but not work. Can you show me how to do it?
Command used and terminal output
No response
Relevant files
No response
System information
No response