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IMGT/GENE-DB downloads failing #273

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mdeboth opened this issue Jul 5, 2023 · 2 comments
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IMGT/GENE-DB downloads failing #273

mdeboth opened this issue Jul 5, 2023 · 2 comments
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@mdeboth
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mdeboth commented Jul 5, 2023

Description of the bug

I'm running nf-core/airrflow for the first time; no IMGT database is cached locally.
It fails with error:

Command error:
  BLAST options error: File igblast_base/fasta/imgt_human_ig_c.fasta is empty
  BLAST options error: File igblast_base/fasta/imgt_human_ig_d.fasta is empty
  BLAST options error: File igblast_base/fasta/imgt_human_ig_j.fasta is empty
  ...
  BLAST options error: File igblast_base/fasta/imgt_aa_mouse_tr_v.fasta is empty

It seems if I try to run the fetch_imgt.sh script manually, wget is failing to download from imgt.org.

@mdeboth mdeboth added the bug Something isn't working label Jul 5, 2023
@mdeboth mdeboth mentioned this issue Jul 6, 2023
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@bshim181
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It seems like the imgt.org database is down currently. I am having the same issue as well. I was wondering if anyone could upload a copy of the previously downloaded data (TR and IG for human).

@mdeboth
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mdeboth commented Jul 10, 2023

Hey @bshim181 - Try running the bin/fetch_imgt.sh script from the dev branch.
Those imgt.org URLs worked for me.

@mdeboth mdeboth closed this as completed Jul 10, 2023
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