Error running demo

[jorvis]

I tried using Bioboxes for the first time using the demo commands. It ran for about 45 seconds before erroring with the trace below:

$ pip2 install --user biobox_cli
[ lots of output, ran successfully ]

$ /home/jorvis/.local/bin/biobox run short_read_assembler bioboxes/megahit --input SRS015996.denovo_duplicates_marked.trimmed.1.fastq --output megahit_test_dir1only
Traceback (most recent call last):
  File "/home/jorvis/.local/bin/biobox", line 9, in <module>
    biobox.run()
  File "/home/jorvis/.local/lib/python2.7/site-packages/biobox_cli/main.py", line 30, in run
    util.select_module("command", opts["<command>"]).run(args)
  File "/home/jorvis/.local/lib/python2.7/site-packages/biobox_cli/command/run.py", line 26, in run
    ctnr = bbx.run(argv)
  File "/home/jorvis/.local/lib/python2.7/site-packages/biobox_cli/biobox_helper.py", line 42, in run
    self.after_run(output, output_dir)
  File "/home/jorvis/.local/lib/python2.7/site-packages/biobox_cli/biobox_type/short_read_assembler.py", line 36, in after_run
    biobox_output = fle.get_biobox_file_contents(host_dst_dir)
  File "/home/jorvis/.local/lib/python2.7/site-packages/biobox_cli/biobox_file.py", line 9, in get_biobox_file_contents
    with open(os.path.join(dir_, 'biobox.yaml'), 'r') as f:
IOError: [Errno 2] No such file or directory: '/tmp/tmpbSgC_Y/biobox.yaml'

[michaelbarton]

Thanks for the bug report Jorvis. Could you tell me what operating system you are using?
Could you also provide the logs of the container you ran? E.g. docker logs ...

[michaelbarton]

The output of docker info would also be helpful. Thanks.

[jorvis]

I'll try to reproduce. I actually just upgraded that laptop to Ubuntu 16.04, so the environment has now changed.

[michaelbarton]

Ok thank you. If you can diagnose the bug that would be very helpful. We
run unit and feature tests on debian so if you do find the cause of the
problem we can try to update the biobox_cli to cover this.

On 3 August 2016 at 08:51, Joshua Orvis notifications@github.com wrote:

I'll try to reproduce. I actually just upgraded that laptop to Ubuntu
16.04, so the environment has now changed.

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[jorvis]

I don't want to drop the ball here, but I did test again on my new OS (Ubuntu 16.04) with a new install of bioboxes and the same issue happened:

$ biobox run short_read_assembler bioboxes/megahit --input SRS015996.denovo_duplicates_marked.trimmed.1.fastq --output megahit_test_dir1only
Traceback (most recent call last):
  File "/usr/local/bin/biobox", line 9, in <module>
    biobox.run()
  File "/usr/local/lib/python2.7/dist-packages/biobox_cli/main.py", line 30, in run
    util.select_module("command", opts["<command>"]).run(args)
  File "/usr/local/lib/python2.7/dist-packages/biobox_cli/command/run.py", line 26, in run
    ctnr = bbx.run(argv)
  File "/usr/local/lib/python2.7/dist-packages/biobox_cli/biobox_helper.py", line 42, in run
    self.after_run(output, output_dir)
  File "/usr/local/lib/python2.7/dist-packages/biobox_cli/biobox_type/short_read_assembler.py", line 36, in after_run
    biobox_output = fle.get_biobox_file_contents(host_dst_dir)
  File "/usr/local/lib/python2.7/dist-packages/biobox_cli/biobox_file.py", line 9, in get_biobox_file_contents
    with open(os.path.join(dir_, 'biobox.yaml'), 'r') as f:
IOError: [Errno 2] No such file or directory: '/tmp/tmph9K5zf/biobox.yaml'

What exact log can I help by sending?

[michaelbarton]

Could you paste the output of docker logs ... using the ID of the
bioboxes/megahit container? You can get this ID using docker ps -a.

Thanks for following up.

[jorvis]

I had tried 'docker ps' and got nothing before posting, but it seems the -a was the critical missing option. OK, the output was:

gzip: /bbx/mount/oB4AnDJr8RR2qrrnq3W0V57z/SRS015996.denovo_duplicates_marked.trimmed.1.fastq: not in gzip format
max_read_len must be greater than 1.

So it appears the megahit biobox requires the input to be in compressed format. It worked after I changed this. Is there a way to get the error to propagate up rather than just showing the YAML error?

[michaelbarton]

Thanks for posting the log and working out what the problem was.

Yes, I agree it would be ideal if the error message was more descriptive. Generally when the biobox.yaml cannot be found it means that something has gone wrong inside the container. A more descriptive error message from the would be useful, perhaps directing the user to look at the container logs if there is a non-zero exit code?

[michaelbarton]

Also to follow up on .gz requirement for the input files, this is one we have added to the biobox specification. This is for expediency as the less input formats we have to support the easier it is to create more bioboxes as less time is required for each.