Error building singularity container

[mezewudo]

I had this error after a while processing the singularity build command:

Error running: enaDataGet -d tmp.7933 -f fasta CVQQ00000000 at /clockwork/scripts/make_pipeline_reference_files.pl line 189.
ABORT: Aborting with RETVAL=255

I do not know what the issue is, it just says something unexpected went wrong, and to try again and if problem persists, ask for assistance.

Thanks for your time.

[pr0xxy]

Same here:

• /clockwork/scripts/make_pipeline_reference_files.pl /clockwork/reference_genomes/
  ------------------- download genomes --------------------
  enaDataGet -d tmp.3901 -f fasta CCBF00000000
  ERROR: Something unexpected went wrong please try again.
  If problem persists, please contact datasubs@ebi.ac.uk for assistance.
  Error running: enaDataGet -d tmp.3901 -f fasta CCBF00000000 at /clockwork/scripts/make_pipeline_reference_files.pl line 190.
  ABORT: Aborting with RETVAL=255
  Cleaning up...

[iqbal-lab]

Sorry for not addressing this sooner. I'll look tomorrow. Cc @martinghunt

[martinghunt]

Strange. I just ran it and it worked for me:

$ ./make_pipeline_reference_files.pl OUT
------------------- download genomes --------------------
wget -nv -O CBMO000000000.fa 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=fasta&retmode=text&id=CBMO000000000'
2019-08-13 18:21:05 URL:https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=fasta&retmode=text&id=CBMO000000000 [1] -> "CBMO000000000.fa" [1]
enaDataGet -d tmp.2481 -f fasta CCBF00000000
Completed
mv tmp.2481/* CCBF00000000.fa.gz
rm -r tmp.2481
enaDataGet -d tmp.2481 -f fasta CWKH00000000
...

[martinghunt]

@pr0xxy did it hang for ages on the line:
enaDataGet -d tmp.3901 -f fasta CCBF00000000
before throwing the error? Or was it instant? I have had it hang on me and had to kill it. (See issue #53).

[mezewudo]

For me it did not hang for long before throwing up the error. But I have run this on multiple occasions and it always fails at the enaDataGet command for some reason.

…

On Tue, Aug 13, 2019 at 2:54 PM martinghunt ***@***.***> wrote: @pr0xxy <https://github.com/pr0xxy> did it hang for ages on the line: enaDataGet -d tmp.3901 -f fasta CCBF00000000 before throwing the error? Or was it instant? I have had it hang on me and had to kill it. (See issue #53 <#53>). — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#52?email_source=notifications&email_token=ABJNQ3Z7VLU22CMTL6VIT23QEL7OHA5CNFSM4IESCWK2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4GUFJQ#issuecomment-520962726>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABJNQ35B5Q2HW4VLBUQT4O3QEL7OHANCNFSM4IESCWKQ> .

[pr0xxy]

@pr0xxy did it hang for ages on the line:
enaDataGet -d tmp.3901 -f fasta CCBF00000000
before throwing the error? Or was it instant? I have had it hang on me and had to kill it. (See issue #53).
Trying to build a singularity image:

git clone https://github.com/iqbal-lab-org/clockwork.git

singularity image.create -s 8000 clockwork_container.img
singularity build clockwork_container.img clockwork_container.def Singularity

The script is called from clockwork_container.def

What am I doing wrong?

[martinghunt]

Are you behind a firewall? Could it be blocking the download?

[pr0xxy]

Are you behind a firewall? Could it be blocking the download?

So I found out the FTP protocol has newly been blocked by our firewall. It seems I will need to find a HTTP mirror. I will update this with what happens.

Thanks,

pr0xxy

[martinghunt]

The URLs are updated for those downloads, and are now HTTP instead of FTP. Please see release 0.7.8 https://github.com/iqbal-lab-org/clockwork/releases/tag/v0.7.8