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treangenlab / emu

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Error with database ncbi_16s_18s_28s #11

Closed aggath closed 5 months ago

aggath commented 5 months ago

Can you please help me with this error? If I choose the ncbi_16S_18S database, the workflow works just fine. But I need the ITS information since I sequenced this region.

Error executing process > 'prepare_databases:download_reference_ref2taxid'

Caused by: Process prepare_databases:download_reference_ref2taxid terminated with an error exit status (4)

Command executed:

wget 'https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS.fna' wget 'https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ref2taxid.ncbi_16s_18s_28s_ITS.tsv' mkdir ncbi_16s_18s_28s_ITS_db mv "ncbi_16s_18s_28s_ITS.fna" ncbi_16s_18s_28s_ITS_db/ mv "ref2taxid.ncbi_16s_18s_28s_ITS.tsv" ncbi_16s_18s_28s_ITS_db/

Command exit status: 4

Command output: (empty)

Command error: --2024-06-14 09:15:02-- https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-metagenomics/ncbi_16s_18s_28s_ITS/ncbi_16s_18s_28s_ITS.fna Resolving ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com (ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com)... failed: Temporary failure in name resolution. wget: unable to resolve host address 'ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com' cp: '.command.out' and '.command.out' are the same file cp: '.command.err' and '.command.err' are the same file cp: '.command.trace' and '.command.trace' are the same file

Work dir: /home/dnasec/epi2melabs/instances/wf-metagenomics_01J0B0EKRWZ2PTPV54QKC9WC68/work/4b/619e8ee056ed47939925b0a70728e5

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

aggath commented 5 months ago

Error was reported in wrong depository.