ERROR ~ Error executing process

[javierAPC]

Description of the bug

Hi, I'm trying to use Sarek from the annotation step. I'm using Linux and Conda. Each time I try, it gives me an error like this:
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (36)'

Caused by:
java.net.SocketTimeoutException: Read timed out

the ouput tells me to check the '.nextflow.log', but it dosen't include what i did today

Command used and terminal output

the input:
nextflow run nf-core/sarek -r 3.4.0 -profile conda --input ./sarek_vcf.csv --outdir ./output --genome GATK.GRCh38 --step annotate --tools merge

the output:

[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX                          -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM1_INDEX                          -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:BWAMEM2_INDEX                          -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE                      -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY         -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN                      -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX                         -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_DBSNP                            -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE                -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS                       -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS                     -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:TABIX_PON                              -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_ALLELES                          -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_LOCI                             -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_GC                               -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_GENOME:UNZIP_RT                               -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED  -
[-        ] process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:BCFTOOLS_MPILEUP       -
[-        ] process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:BAM_NGSCHECKMATE:NGSCHECKMATE_NCM       -
[-        ] process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS               -
[-        ] process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT          -
[-        ] process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL           -
[-        ] process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY             -
[-        ] process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF    -
[-        ] process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX -
[-        ] process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP    -
[-        ] process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:TABIX_TABIX       -
[-        ] process > NFCORE_SAREK:SAREK:CUSTOM_DUMPSOFTWAREVERSIONS                           -
[-        ] process > NFCORE_SAREK:SAREK:MULTIQC                                               -
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (36)'

Caused by:
  java.net.SocketTimeoutException: Read timed out


 -- Check '.nextflow.log' file for details

UPTADE:
i tried the -profile test and this error pop out:

"Caused by:
Failed to create Conda environment
command: conda env create --prefix /media/victor/c1d5c312-b546-4d5e-b24f-72dbe9e6f18f/javier_CPTAC/WGS/raw_data/work/conda/gawk-f9b4f646bf1b67e52890543d27cb2f27 --file /home/victor/.nextflow/assets/nf-core/sarek/./workflows/../subworkflows/local/prepare_intervals/../../../modules/local/create_intervals_bed/environment.yml
status : 1
message:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working...
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.

Building graph of deps:   0%|          | 0/5 [00:00<?, ?it/s]
Examining libgcc-ng[version='>=7.3.0']:   0%|          | 0/5 [00:00<?, ?it/s]
Examining @/linux-64::__unix==0=0:  20%|██        | 1/5 [00:00<00:00, 34.65it/s]
Examining @/linux-64::__glibc==2.36=0:  40%|████      | 2/5 [00:00<00:00, 69.12it/s]
Examining @/linux-64::__archspec==1=cascadelake:  60%|██████    | 3/5 [00:00<00:00, 103.50it/s]
Examining @/linux-64::__linux==6.1.0=0:  80%|████████  | 4/5 [00:00<00:00, 137.77it/s]         
                                                                                      

Determining conflicts:   0%|          | 0/5 [00:00<?, ?it/s]
Examining conflict for __glibc libgcc-ng:   0%|          | 0/5 [00:00<?, ?it/s]
                                                                               
failed
Solving environment: ...working... 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.

Building graph of deps:   0%|          | 0/5 [00:00<?, ?it/s]
Examining libgcc-ng[version='>=7.3.0']:   0%|          | 0/5 [00:00<?, ?it/s]
Examining @/linux-64::__unix==0=0:  20%|██        | 1/5 [00:00<00:00, 38.52it/s]
Examining @/linux-64::__glibc==2.36=0:  40%|████      | 2/5 [00:00<00:00, 76.77it/s]
Examining @/linux-64::__archspec==1=cascadelake:  60%|██████    | 3/5 [00:00<00:00, 114.93it/s]
Examining @/linux-64::__linux==6.1.0=0:  80%|████████  | 4/5 [00:00<00:00, 152.95it/s]         
                                                                                      

Determining conflicts:   0%|          | 0/5 [00:00<?, ?it/s]
Examining conflict for __glibc libgcc-ng:   0%|          | 0/5 [00:00<?, ?it/s]
                                                                               
failed

UnsatisfiableError: The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.36=0
  - libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.36

Note that strict channel priority may have removed packages required for satisfiability.

-- Check '.nextflow.log' file for details
"

Relevant files

No response

System information

Nextflow version: 23.10.1 build 5891
System: Linux 6.1.0-12-amd64 x86_64
Version of nf-core/sarek (3.4.0)

[maxulysse]

Can you share the .nextflow.log file?

[javierAPC]

Okay, so i was looking the wrong log file.
The right one have this last lines.

"abr-03 12:33:18.282 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-amazon@2.1.4'
abr-03 12:33:18.282 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-amazon
abr-03 12:33:18.282 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-prov@1.2.2'
abr-03 12:33:18.282 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-prov
abr-03 12:33:18.282 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-validation@1.1.3'
abr-03 12:33:18.282 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation

abr-03 12:33:18.310 [FileTransfer-9] DEBUG nextflow.cloud.aws.nio.S3Client - S3 download file: s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz interrupted

abr-03 12:33:18.310 [FileTransfer-8] DEBUG nextflow.cloud.aws.nio.S3Client - S3 download file: s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz interrupted

abr-03 12:33:18.310 [FileTransfer-1] DEBUG nextflow.cloud.aws.nio.S3Client - S3 download file: s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz interrupted

abr-03 12:33:18.310 [FileTransfer-10] DEBUG nextflow.cloud.aws.nio.S3Client - S3 download file: s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz interrupted

abr-03 12:33:18.311 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

abr-03 12:33:18.317 [S3TransferManager-4] WARN c.a.s.s.i.S3AbortableInputStream - Not all bytes were read from the S3ObjectInputStream, aborting HTTP connection. This is likely an error and may result in sub-optimal behavior. Request only the bytes you need via a ranged GET or drain the input stream after use.

abr-03 12:33:18.317 [S3TransferManager-10] WARN c.a.s.s.i.S3AbortableInputStream - Not all bytes were read from the S3ObjectInputStream, aborting HTTP connection. This is likely an error and may result in sub-optimal behavior. Request only the bytes you need via a ranged GET or drain the input stream after use."

Honestly i dont know what to do