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This maybe nothing at all but maybe important to mention in the documentation, that this process may require restart...
At the download genome assemblies step, I got this error:
ERROR ~ Error executing process > 'NFCORE_PLANTPATHSURVEIL:PLANTPATHSURVEIL:DOWNLOAD_REFERENCES:DOWNLOAD_ASSEMBLIES (GCA_016864655.1)'
Caused by:
Process `NFCORE_PLANTPATHSURVEIL:PLANTPATHSURVEIL:DOWNLOAD_REFERENCES:DOWNLOAD_ASSEMBLIES (GCA_016864655.1)` terminated with an error exit status (2)
Command executed:
# Download assemblies as zip archives
datasets download genome accession GCA_016864655.1 --include gff3,rna,cds,protein,genome,seq-report --filename GCA_016864655.1.zip
# Unzip
unzip GCA_016864655.1.zip
# Rename files with assembly name
if [ -f ncbi_dataset/data/GCA_016864655.1/genomic.gff ]; then
mv ncbi_dataset/data/GCA_016864655.1/genomic.gff ncbi_dataset/data/GCA_016864655.1/GCA_016864655.1.gff
fi
if [ -f ncbi_dataset/data/GCA_016864655.1/cds_from_genomic.fna ]; then
mv ncbi_dataset/data/GCA_016864655.1/cds_from_genomic.fna ncbi_dataset/data/GCA_016864655.1/GCA_016864655.1_cds.fna
fi
if [ -f ncbi_dataset/data/GCA_016864655.1/protein.faa ]; then
mv ncbi_dataset/data/GCA_016864655.1/protein.faa ncbi_dataset/data/GCA_016864655.1/GCA_016864655.1.faa
fi
cat <<-END_VERSIONS > versions.yml
"NFCORE_PLANTPATHSURVEIL:PLANTPATHSURVEIL:DOWNLOAD_REFERENCES:DOWNLOAD_ASSEMBLIES":
datasets: $(datasets --version | sed -e "s/datasets version: //")
END_VERSIONS
Command exit status:
2
Command output:
Archive: GCA_016864655.1.zip
inflating: README.md
inflating: ncbi_dataset/data/assembly_data_report.jsonl
inflating: ncbi_dataset/data/GCA_016864655.1/GCA_016864655.1_ASM1686465v1_genomic.fna
inflating: ncbi_dataset/data/GCA_016864655.1/genomic.gff inflating: ncbi_dataset/data/GCA_016864655.1/cds_from_genomic.fna
inflating: ncbi_dataset/data/GCA_016864655.1/protein.faa
inflating: ncbi_dataset/data/GCA_016864655.1/sequence_report.jsonl
inflating: ncbi_dataset/data/dataset_catalog.json
Collecting 1 records [================================================] 100% 1/1
Downloading: GCA_016864655.1.zip 41MB done
Archive: GCA_016864655.1.zip
inflating: README.md
inflating: ncbi_dataset/data/assembly_data_report.jsonl
inflating: ncbi_dataset/data/GCA_016864655.1/GCA_016864655.1_ASM1686465v1_genomic.fna
inflating: ncbi_dataset/data/GCA_016864655.1/genomic.gff
error: invalid compressed data to inflate
inflating: ncbi_dataset/data/GCA_016864655.1/cds_from_genomic.fna
inflating: ncbi_dataset/data/GCA_016864655.1/protein.faa
inflating: ncbi_dataset/data/GCA_016864655.1/sequence_report.jsonl
inflating: ncbi_dataset/data/dataset_catalog.json
Work dir:
/nfs7/BPP/Chang_Lab/paradarc/nf_brady_N120/scripts/nf-core-plantpathsurveil/work/00/7f5d8df6693888570725145aa13835
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '.nextflow.log' file for details
It could be that it is a glitch on the download or unzip process. I ran it again (-resume) and the download works just fine.
Command used and terminal output
No response
Relevant files
No response
System information
No response
The text was updated successfully, but these errors were encountered:
I added code for that step to be retried up to some number of times and then just not include that reference and continue if it fails too many times. I think it helped with a lot of those random internet connection related errors.
Description of the bug
This maybe nothing at all but maybe important to mention in the documentation, that this process may require restart...
At the download genome assemblies step, I got this error:
It could be that it is a glitch on the download or unzip process. I ran it again (-resume) and the download works just fine.
Command used and terminal output
No response
Relevant files
No response
System information
No response
The text was updated successfully, but these errors were encountered: