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kircherlab / CADD-scripts

CADD scripts release for offline scoring. For more information about CADD, please visit our website
http://cadd.gs.washington.edu
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annotation error #50

Closed Mong-yj closed 2 months ago

Mong-yj commented 7 months ago

Hi,

I executed the command "./CADD.sh test/input.vcf" and got the following error.

""" Activating conda environment: envs/56b93169d3e29fd592952535267703b3_ [E::hts_hopen] Failed to open file /home/user/CADD-scripts-1.6.post1/data/annotations/GRCh38_v1.6//phastCons/hg38.phastCons.bg.gz [E::hts_open_format] Failed to open file "/home/user/CADD-scripts-1.6.post1/data/annotations/GRCh38_v1.6//phastCons/hg38.phastCons.bg.gz" : Exec format error Traceback (most recent call last): File "/home/user/CADD-scripts-1.6.post1/src/scripts/annotateVEPvcf.py", line 94, in annotation.load(args) File "/home/user/script/CADD-scripts-1.6.post1/src/scripts/lib/Annotations.py", line 30, in load self.tabix = pysam.TabixFile(self.path,'r'),None,None,None,None,None,None,"%s annotation" % self.name File "pysam/libctabix.pyx", line 350, in pysam.libctabix.TabixFile.cinit File "pysam/libctabix.pyx", line 391, in pysam.libctabix.TabixFile._open IOError: could not open file /home/user/CADD-scripts-1.6.post1/data/annotations/GRCh38_v1.6//phastCons/hg38.phastCons.bg.gz """

The same error for another file occurred when the command "./CADD.sh -a -g GRCh37 -o output_inclAnno_GRCh37.tsv.gz test/input.vcf" of version GRCh37.

""" IOError: could not open file /home/user/CADD-scripts-1.6.post1/data/annotations/GRCh37_v1.6//mutation_density/mutDensity_gnomAD/variant_density.gnomad.2.0.1.100.bg.gz """

If I open the file in that location directly, it will open normally. What's the problem?

Thank you.

visze commented 2 months ago

Please reopen if it is still relevant.