libcurl ssl issue
barslmn opened this issue · 2 comments
barslmn commented
Hi,
I had a similar error to #45.
versions:
debian: unstable
igv-reports 1.9.1
(venv) bar@debiantestin:~/runs/results.282091$ create_report $OUTPUT.bcf --genome hg38 --flanking 1000 --info-columns CSQ --tracks $OUTPUT.cram -
-output $OUTPUT.html
[E::easy_errno] Libcurl reported error 77 (Problem with the SSL CA cert (path? access rights?))
[E::hts_open_format] Failed to open file "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz" : Input/output error
[E::easy_errno] Libcurl reported error 77 (Problem with the SSL CA cert (path? access rights?))
[E::fai_load3_core] Failed to open FASTA index https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa.fai: Input/output error
Traceback (most recent call last):
File "/home/bar/venv/bin/create_report", line 8, in <module>
sys.exit(main())
^^^^^^
File "/home/bar/venv/lib/python3.11/site-packages/igv_reports/report.py", line 503, in main
create_report(args)
File "/home/bar/venv/lib/python3.11/site-packages/igv_reports/report.py", line 109, in create_report
session_dict = json.dumps(create_session_dict(args, table, trackjson))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/bar/venv/lib/python3.11/site-packages/igv_reports/report.py", line 179, in create_session_dict fasta_reader = FastaReader(args.fasta)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/bar/venv/lib/python3.11/site-packages/igv_reports/fasta.py", line 31, in __init__
self.fasta = pysam.FastaFile(file)
^^^^^^^^^^^^^^^^^^^^^
File "pysam/libcfaidx.pyx", line 121, in pysam.libcfaidx.FastaFile.__cinit__
File "pysam/libcfaidx.pyx", line 181, in pysam.libcfaidx.FastaFile._open
OSError: error when opening file `https://igv-genepattern-org.s3.amazonaws.com/genomes/seq/hg38/hg38.fa`
This solved my issue:
sudo apt install libcurl4-openssl-dev
Using the http url to reference genome solves the issue.
I still got this error but expected report was created.
[E::easy_errno] Libcurl reported error 77 (Problem with the SSL CA cert (path? access rights?))
[E::hts_open_format] Failed to open file "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz" : Input/output error
jrobinso commented
I'm not sure what's going on there but I can't detect anything wrong with the ssl certificates for any of the urls posted. They download fine via https from a web browser. I do recall some posts about SSL problems with certain versions of Libcurl.
mohamedsinanm commented
export CURL_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt solved the issue for me pysam-developers/pysam#1268