Stopping! Signal received: 13

[schultzm]

Hi,

Thanks for writing the very useful Ariba.

During my recent use of version 2.12.1, Ariba finished successfully; however, if I don't use the --verbose option, the last message I see (printed to stdout, line 196) is Stopping! Signal received: 13. From what I can tell, this means:

      SIGPIPE      13       Term    Broken pipe: write to pipe with no
                                     readers; see pipe(7)

Are you able to confirm that this is the correct behaviour? If it is, can you please hide this message? Else, can you tell me what is going wrong?

Thanks,

[martinghunt]

Ignore it. I think it started happening after multithreading for bowtie2 and spades was added back in as an option (#210). Sorry, I don't what's causing that to be output.

[JFsanchezherrero]

Hi there,
Should I worry about receiving this signal in my data? Has ariba finished succesfully or should I tried again?
Thanks

[kpepper]

Where abouts in the log does it appear?

[JFsanchezherrero]

Hi there,
As it makes ariba to stop it appears at the end of the log. But I don't know if it finished properly. Basically, no other messages are provided.

The command I sent was:

ariba run --threads 8 VFDB_data sample_R1.fastq sample_R2.fastq output_example

Head of the log file:

adsA detected 1 threads available to it
cap8B detected 1 threads available to it
cap8E detected 1 threads available to it
....

Tail of the log file:

....
sdrC reported completion
sdrE reported completion
sea detected 8 threads available to it
sea reported completion
Stopping! Signal received: 13

No further details were provided and no any other messages were prompt.
Jose

[kpepper]

Hi @JFsanchezherrero, if you get all the report tsv files it should be okay. However, if you're concerned then you could always try the latest version - v2.13.5 from PyPI or Bioconda, or use the Docker image which has all the dependencies bundled in:

docker pull sangerpathogens/ariba

Instructions for this are on there Github pages/Wiki.

[JFsanchezherrero]

Thanks.
I will take a look.

[kpepper]

FYI, release v2.14.1 includes a fix for this "Stopping" issue.

[JFsanchezherrero]

Dear developers,

I successfully update ariba within my environment using

pip install --upgrade ariba

(my_env) jsanchez@cacau:/my_folder/test$ pip install --upgrade ariba
Collecting ariba
  Downloading https://files.pythonhosted.org/packages/fd/ff/be0df07ed469cb55e951fda3cf81102f54729a253f2dacdb719831abb8a2/ariba-2.14.1.tar.gz (2.7MB)
    100% |████████████████████████████████| 2.7MB 749kB/s 
Requirement already satisfied, skipping upgrade: BeautifulSoup4>=4.1.0 in /my_env/lib/python3.5/site-packages (from ariba) (4.7.1)
Requirement already satisfied, skipping upgrade: biopython in /my_env/lib/python3.5/site-packages (from ariba) (1.73)
Requirement already satisfied, skipping upgrade: dendropy>=4.2.0 in /my_env/lib/python3.5/site-packages (from ariba) (4.4.0)
Requirement already satisfied, skipping upgrade: matplotlib in /my_env/lib/python3.5/site-packages (from ariba) (2.2.4)
Requirement already satisfied, skipping upgrade: pyfastaq>=3.12.0 in /my_env/lib/python3.5/site-packages (from ariba) (3.17.0)
Requirement already satisfied, skipping upgrade: pysam>=0.9.1 in /my_env/lib/python3.5/site-packages (from ariba) (0.15.2)
Requirement already satisfied, skipping upgrade: pymummer<=0.10.3 in /my_env/lib/python3.5/site-packages (from ariba) (0.10.3)
Requirement already satisfied, skipping upgrade: soupsieve>=1.2 in /my_env/lib/python3.5/site-packages (from BeautifulSoup4>=4.1.0->ariba) (1.9)
Requirement already satisfied, skipping upgrade: numpy in /my_env/lib/python3.5/site-packages (from biopython->ariba) (1.16.4)
Requirement already satisfied, skipping upgrade: setuptools in /my_env/lib/python3.5/site-packages (from dendropy>=4.2.0->ariba) (41.0.0)
Requirement already satisfied, skipping upgrade: cycler>=0.10 in /my_env/lib/python3.5/site-packages (from matplotlib->ariba) (0.10.0)
Requirement already satisfied, skipping upgrade: python-dateutil>=2.1 in /my_env/lib/python3.5/site-packages (from matplotlib->ariba) (2.8.0)
Requirement already satisfied, skipping upgrade: pytz in /my_env/lib/python3.5/site-packages (from matplotlib->ariba) (2018.9)
Requirement already satisfied, skipping upgrade: six>=1.10 in /my_env/lib/python3.5/site-packages (from matplotlib->ariba) (1.12.0)
Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /my_env/lib/python3.5/site-packages (from matplotlib->ariba) (2.4.0)
Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /my_env/lib/python3.5/site-packages (from matplotlib->ariba) (1.0.1)
ariba 2.14.1 has requirement matplotlib>=3.1.0, but you'll have matplotlib 2.2.4 which is incompatible.
Installing collected packages: ariba
  Found existing installation: ariba 2.13.5
    Uninstalling ariba-2.13.5:
      Successfully uninstalled ariba-2.13.5
  Running setup.py install for ariba ... done
Successfully installed ariba-2.14.1

But the thing is if I try to use ariba it keeps on complaining.

(my_env) jsanchez@cacau:/my_folder/test$ ariba -h
Traceback (most recent call last):
  File "/my_env/bin/ariba", line 3, in <module>
    import ariba
  File "/my_env/lib/python3.5/site-packages/ariba/__init__.py", line 57, in <module>
    from ariba import *
  File "/my_env/lib/python3.5/site-packages/ariba/ref_genes_getter.py", line 614
    print(f"E-fetching {len(acc_list)} genbank records from BioProject {BIOPROJECT} and writing to.  This may take a while.", file=sys.stderr)
                                                                                                                           ^
SyntaxError: invalid syntax

Is it because there is the dependency on matplolib that is not fulfilled? Or is it related to the new content you added it?

Thanks.

[kpepper]

It needs Python 3.6 now - try upgrading Python version to 3.6 and see if that helps.

[JFsanchezherrero]

Thank you very much for that quick response.
I will let you know when I could have Python 3.6 in the system, depends on IT dept.

[kpepper]

As stated previously, release v2.14.1+ includes a fix for this issue.