Error building the databases(HGNC,FUSIONREPORT_DOWNLOAD,FUSIONCATCHER_DOWNLOAD, STAR_GENOMEGENERATE)

[usama-khan1998]

I am running the build database command and the following databases are not downloading, such as HGNC, FUSIONCATCHER_DOWNLOAD, STAR_GENOMEGENERATE. I dont know how to resolve this issue.

(env_nf) ngs@NGS:~$ nextflow run nf-core/rnafusion -profile docker --build_references --all --cosmic_username ******************* --cosmic_passwd ********** --genomes_base /home/ngs/apps/rna_fusion --outdir /home/ngs/apps/references

N E X T F L O W ~ version 24.10.4

Launching https://github.com/nf-core/rnafusion [backstabbing_church] DSL2 - revision: f27e732 [master]

WARN: Access to undefined parameter monochromeLogs -- Initialise it to a default value eg. params.monochromeLogs = some_value

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|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,'
nf-core/rnafusion v3.0.2-gf27e732

Core Nextflow options
revision : master
runName : backstabbing_church
containerEngine : docker
launchDir : /home/ngs
workDir : /home/ngs/work
projectDir : /home/ngs/.nextflow/assets/nf-core/rnafusion
userName : ngs
profile : docker
configFiles :

Input/output options
input : https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv
outdir : /home/ngs/apps/references
build_references : true
cosmic_username : *******************
cosmic_passwd : *************
genomes_base : /home/ngs/apps/rna_fusion
starfusion_build : true
all : true
arriba_ref : /home/ngs/apps/rna_fusion/arriba
arriba_ref_blacklist : /home/ngs/apps/rna_fusion/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz
arriba_ref_cytobands : /home/ngs/apps/rna_fusion/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv
arriba_ref_known_fusions : /home/ngs/apps/rna_fusion/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz
arriba_ref_protein_domains : /home/ngs/apps/rna_fusion/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3
ensembl_ref : /home/ngs/apps/rna_fusion/ensembl
fusioncatcher_limitSjdbInsertNsj : 2000000
fusioncatcher_ref : /home/ngs/apps/rna_fusion/fusioncatcher/human_v102
fusioninspector_limitSjdbInsertNsj: 1000000
fusionreport_ref : /home/ngs/apps/rna_fusion/fusion_report_db
hgnc_ref : /home/ngs/apps/rna_fusion/hgnc/hgnc_complete_set.txt
hgnc_date : /home/ngs/apps/rna_fusion/hgnc/HGNC-DB-timestamp.txt
starfusion_ref : /home/ngs/apps/rna_fusion/starfusion/ctat_genome_lib_build_dir
starindex_ref : /home/ngs/apps/rna_fusion/star
tools_cutoff : 1

Read trimming options
adapter_fasta : []

Alignment compression options
cram : []

Reference genome options
genome : GRCh38
fasta : /home/ngs/apps/rna_fusion/ensembl/Homo_sapiens.GRCh38.102.all.fa
fai : /home/ngs/apps/rna_fusion/ensembl/Homo_sapiens.GRCh38.102.all.fa.fai
gtf : /home/ngs/apps/rna_fusion/ensembl/Homo_sapiens.GRCh38.102.gtf
chrgtf : /home/ngs/apps/rna_fusion/ensembl/Homo_sapiens.GRCh38.102.chr.gtf
transcript : /home/ngs/apps/rna_fusion/ensembl/Homo_sapiens.GRCh38.102.cdna.all.fa.gz
refflat : /home/ngs/apps/rna_fusion/ensembl/Homo_sapiens.GRCh38.102.chr.gtf.refflat
rrna_intervals : /home/ngs/apps/rna_fusion/ensembl/Homo_sapiens.GRCh38.102.interval_list

!! Only displaying parameters that differ from the pipeline defaults !!

If you use nf-core/rnafusion for your analysis please cite:

• The pipeline

• The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

• Software dependencies
  https://github.com/nf-core/rnafusion/blob/master/CITATIONS.md

---

executor > local (5)
[09/5bff6c] process > NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD (ensembl) [100%] 1 of 1 ✔
[70/35d4f1] process > NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc) [100%] 1 of 1, failed: 1 ✘
[- ] process > NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX -
[- ] process > NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY -
[- ] process > NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS -
[- ] process > NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED -
[- ] process > NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST -
[- ] process > NFCORE_RNAFUSION:BUILD_REFERENCES:STAR_GENOMEGENERATE -
[8a/55fb51] process > NFCORE_RNAFUSION:BUILD_REFERENCES:ARRIBA_DOWNLOAD (arriba) [100%] 1 of 1 ✔
[1e/19d914] process > NFCORE_RNAFUSION:BUILD_REFERENCES:FUSIONCATCHER_DOWNLOAD (fusioncatcher_download) [ 0%] 0 of 1
[- ] process > NFCORE_RNAFUSION:BUILD_REFERENCES:STARFUSION_BUILD -
[- ] process > NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT -
[83/2bd795] process > NFCORE_RNAFUSION:BUILD_REFERENCES:FUSIONREPORT_DOWNLOAD (fusionreport) [100%] 1 of 1, failed: 1 ✘

ERROR ~ Error executing process > 'NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc)'

Caused by:
Process NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc) terminated with an error exit status (8)

Command executed:

wget https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt
date +%Y-%m-%d/%H:%M > HGNC-DB-timestamp.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD":
wget: $(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3 > versions.yml)
END_VERSIONS

Command exit status:
8

Command output:
(empty)

Command error:
--2025-01-23 04:36:22-- https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt
Resolving ftp.ebi.ac.uk... 193.62.193.165
Connecting to ftp.ebi.ac.uk|193.62.193.165|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2025-01-23 04:36:23 ERROR 404: Not Found.

Work dir:
/home/ngs/work/70/35d4f11c4567e843f91630cd46483a

Container:
quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

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

[Inaselsayed]

I'm in the middle of the same issue. I have seen that this has been flagged as a bug in Github, still couldn't find out how to solve it. I tried to edit the main.nf with the working URL, but it didn't work!