temp file attribute error

[slschnorr]

Hi, apologies that this is probably user error in my environment, but when I attempt to run parallel-fastq-dump using this command:

parallel-fastq-dump --sra-id SRR1930123 --threads 4 --outdir ./ --split-files --gzip

I get this error (with traceback):

Traceback (most recent call last): File "/usr/bin/parallel-fastq-dump", line 100, in <module> main() File "/usr/bin/parallel-fastq-dump", line 93, in main pfd(args, si, extra_args, n_spots) File "/usr/bin/parallel-fastq-dump", line 12, in pfd tmp_dir = tempfile.TemporaryDirectory(prefix="pfd_",dir=args.tmpdir) AttributeError: 'module' object has no attribute 'TemporaryDirectory'

I'm running this in centos, and I noticed that the shebang of the parallel-fastq-dump script is calling for python2: #!/usr/bin/python2
Is this an error? I installed with pip install, and version is 0.6.2. Thanks for your help!

[rvalieris]

hello,

the problem is that TemporaryDirectory function only exists in python 3. can you use python3 instead of python2 ?

if not, one workaround would be to install the backports.tempfile package and then replace import tempfile on the script with from backports import tempfile.

[slschnorr]

Thanks for the fast response! I just installed python3, so I will change the shebang on your file to:
#!/usr/bin/python3
or is it instead correct to do:
#!/usr/bin/env python3
?

[rvalieris]

both work fine, given that python3 is in /usr/bin, but the second is generally better.

[slschnorr]

Great, I think it is working now. Thank you for your help!

[rvalieris]

no problem ! glad I could help.