Skip to content

Error building index #21

@pdtrang

Description

@pdtrang

Hi,

I try to run hera_build but it keeps giving me the following error.

`./hera_build --fasta /home/user/test_data/Homo_sapiens.GRCh37.87.fa --gtf /home/user/test_data/Homo_sapiens.GRCh37.87.gtf --outdir /home/user/test_data --full_index 0 --grch38 0

Scan reference sequence ...
Scan gtf file...
Extract transcript sequence
Traceback (most recent call last):
File "/usr/bin/hera_build", line 230, in
subprocess.call([path , "index", "-t", os.path.join(args.outdir, "transcripts.fasta"), "-o", os.path.join(args.outdir, "index"), "-g", args.fasta])
File "/usr/lib/python2.7/subprocess.py", line 523, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib/python2.7/subprocess.py", line 711, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
`
I'm not sure which file hera looked for. Please let me know how to fix it.

Thanks!

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions