Abbys not working

Question: Abbys not working - error

3.1 years ago by

vebaev • 130

vebaev • 130 wrote:

I have installed from the tools shed Abbys (1.9.0 latest version) with no errors, nevertheless after executing a job abbys returns error: (with command line Abbys is working fine with the same FASTQ file)

Fatal error: Exit code 2 ()
`/export/galaxy-central/database/files/000/dataset_102.dat': discarded 19401 reads containing non-ACGT characters
The minimum coverage of single-end contigs is 2.
The minimum coverage of merged contigs is 2.
Building the suffix array...
Building the Burrows-Wheeler transform...
Building the character occurrence table...
Mateless         0
Unaligned  3714651  44.4%
Singleton  1517910  18.1%
FR         1451668  17.4%
RF              14  0.000167%
FF              12  0.000143%
Different  1681281  20.1%
Total      8365536
Reading `abyss-3.fa'...
Writing `abyss-3.fa.fai'...
Reading `abyss-4.fa'...
Writing `abyss-4.fa.fai'...
Ambiguous paths: 7
Merged:          4
No paths:        0
Too many paths:  3
Too complex:     0
Dissimilar:      0
The minimum coverage of single-end contigs is 1.44898.
The minimum coverage of merged contigs is 3.55215.
Consider increasing the coverage threshold parameter, c, to 3.55215.
Building the suffix array...
Building the Burrows-Wheeler transform...
Building the character occurrence table...
Mateless         0
Unaligned  3714387  44.4%
Singleton  1514302  18.1%
FR         1492709  17.8%
RF              57  0.000681%
FF              15  0.000179%
Different  1644066  19.7%
Total      8365536
n	n:200	L50	min	N80	N50	N20	E-size	max	sum	name
294019	11456	3289	200	217	268	833	6547	81856	3689394
Ambiguous paths: 13
Merged:          4
No paths:        4
Too many paths:  3
Too complex:     0
Dissimilar:      2
The minimum coverage of single-end contigs is 1.44898.
The minimum coverage of merged contigs is 2.13846.
Consider increasing the coverage threshold parameter, c, to 2.13846.
/galaxy-central/tool_deps/abyss/1.9.0/iuc/package_abyss_1_9_0/09f111573a77/bin/abyss-tabtomd: 12: /galaxy-central/tool_deps/abyss/1.9.0/iuc/package_abyss_1_9_0/09f111573a77/bin/abyss-tabtomd: column: not found
awk: close failed on file /dev/stdout (Broken pipe)
make: *** [abyss-stats.md] Error 127
make: *** Deleting file `abyss-stats.md'

abbys galaxy local • 741 views

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modified 3.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.1 years ago by vebaev • 130

3.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This looks like a dependency issue. Was this tool installed with "managed dependencies" and are those all OK when you examine them in the Admin panel? If not or are not sure, you can delete the tool and re-install. All dependencies must be available to the Galaxy user. If using resources that were already available on your server, double check that the location of these are in the $PATH.

https://wiki.galaxyproject.org/Admin/Config/ToolDependencies

The IUC will likely jump in and comment more if I am totally off base. Thanks, Jen, Galaxy team

ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

All items under "Manage installed tools" are listed as Installed in green!?

ADD REPLY • link written 3.1 years ago by vebaev • 130

Hum. If you go into the ABySS tool and examine the dependencies listed, are all installed correctly there? If they were never attempted to be installed through the Tool Shed, then these won't show up under this view. If this does not work, you can either wait for someone who developed the tool wrapper to help here or contact them directly through the Tool Shed.

That said, this could still be a usage issue and not a Galaxy/tool issue. Sparse data keeps coming to mind since other tools will sometimes error out in a somewhat similar way when this the case. For the majority, the problem is generally traced back to poor input sequence format (specifically, the quality score scaling but sometimes the length/quality of the reads vs the tool parameters). You can check for those things, but it is purely a guess. The defaults on the command-line versus the tool wrapper can differ, as can the input requirements.

Asking the question to the tool author directly is another path. The google group is here:
https://groups.google.com/forum/#!forum/abyss-users

ADD REPLY • link modified 3.1 years ago • written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

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