igv-reports: Not able to find reference on s3.amazon

When I run any of the two examples I get the following error:

create_report examples/junctions/Introns.38.bed \
    https://s3.dualstack.us-east-1.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa \
    --type junction \
    --ideogram examples/junctions/cytoBandIdeo.txt \
    --output junctions.html \
    --track-config examples/junctions/tracks.json \
    --info-columns TCGA GTEx variant_name \
    --title "Sample A"

Traceback (most recent call last):
  File "/home/daniel/miniconda3/bin/create_report", line 8, in <module>
    sys.exit(main())
  File "/home/daniel/miniconda3/lib/python3.8/site-packages/igv_reports/report.py", line 234, in main
    create_report(args)
  File "/home/daniel/miniconda3/lib/python3.8/site-packages/igv_reports/report.py", line 87, in create_report
    data = fasta.get_data(args.fasta, region)
  File "/home/daniel/miniconda3/lib/python3.8/site-packages/igv_reports/fasta.py", line 21, in get_data
    fasta = pysam.FastaFile(fasta_file)
  File "pysam/libcfaidx.pyx", line 123, in pysam.libcfaidx.FastaFile.__cinit__
  File "pysam/libcfaidx.pyx", line 155, in pysam.libcfaidx.FastaFile._open
OSError: file `https://s3.dualstack.us-east-1.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa` not found

About this issue

Original URL
State: closed
Created 4 years ago
Comments: 21 (12 by maintainers)

Commits related to this issue

Update readme instructions to use http: protocol for s3 resources. Work around for possible linux/libcurl bug. See issue #45. — committed to igvteam/igv-reports by jrobinso 2 years ago

Most upvoted comments

This looks like a libcurl bug affecting SSL certificates, there is nothing wrong with the certificate for that file. A workaround is to use an http url (instead of https). Specifically

http://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa

I don’t know anything about singularity, but here is a Colab notebook with that example (working). I will update the readme to use http: https://colab.research.google.com/drive/1JJvyDm0r_Lyhmuk27zEwfkE0J1gV0wzp?usp=sharing

jrobinso on Mar 18, 2022