binner segment fault

[Sanrrone]

Dears, doing the usage (using blast), and the files that you provide in

https://elefant.bifo.helmholtz-hzi.de/public.php?service=files&t=5b8a18c97921b0233adb2904b7945726
(I select the virus sample)

doing:

cat test+tab |taxator -g mapping.tax -q 1.fa -v 1.fa.fai -f refdata.fna -i ref.fna.fai -p 16 | sort -k1,1 > my.predictions.gff3

finish ok, But the next step, using binner the software crash

cat my.predictions.gff3 |binner
terminate called after throwing an instance of 'boost::exception_detail::clone_implboost::exception_detail::error_info_injector<boost::program_options::required_option >'
what(): the option '--sample-identifier' is required but missing
Aborted (core dumped)

which is that identifier file?
i tried the fai,dmp from taxonomy, and both give segment fault (core dumped) error.

Regards

[fungs]

Hello Sandro,

the sample identifier is a string which you must pass via the command line. The CAMI binning format has a mandatory identifier in the header:

https://github.com/bioboxes/rfc/blob/4bb19a633a6a969c2332f1f298852114c5f89b1b/data-format/binning.mkd

The purpose of this identifier is to record unambiguously the data sample that you have processed, other than using a file name or external metadata.

You can always use the --help command line switch to see which parameters are required by any of the taxator-tk binaries. Also, you can look into the pipeline scripts in the extended versions and how they call the different programs.

Gruß Johannes

[Sanrrone]

thanks funds, layer 8 error, just an string for header output binner, the problem is that the same binner give me a segment fault error:

cat my.predictions.gff3 |binner -n "testID"
Segmentation fault (core dumped)

I did not find anything unusual in my gff (i attached the file).
what can i do?

thanks in advanced

my.predictions.gff3.zip

[fungs]

Hi, I ran the binner binary from the extended package 1.3.3e with your attached gff3 file and the taxonomy which is contained in the refpack refseq-viral_67:

binner -n "testID" < my.predictions.gff3 > my.predictions.binning
analyzing sample composition by signal counting... done: 49 nested taxa with total support of 29626 bp
noise removal... done: 0 taxa were removed
binning step...  done

I did not get a segfault. Please make sure to run the same commands and check the logfile (default binning.log) for errors. I the problem persists, please report the exact version of the binner, for instance the git commit or release. We recommend to not use development but only the released versions.

Gruß Johannes

[Sanrrone]

thanks @fungs, the tip with the binner versions works for me, I was using the lastet development version (cloning the repository), using last release (1.3.3), and the same command, works fine.

[fungs]

Still needs to be fixed...

[fungs]

Fix will be in next release, give meaningful error when -n argument is not given.