Error on all the "gotcha-" Classifications

[gmoore777]

(I'm brand new to Edge, etc.)

I installed Edge on Linux Ubuntu 18.04 (and had several issues that I plowed through)

and I am not sure if part of the installation did not go well in regards

to the results below.

I ran Edge, using:

         Input Source: NCBI SRA
         SRA Accession: SRX3660496

 and accepted all the defaults.

After 22 minutes, the summary report was chock full of information, but had

some "Error" results in red:

Reads Taxononmy Classification:

gottcha-genDB-b    On    Error    00:00:30
gottcha-genDB-v    On    Error    00:00:01
gottcha-speDB-b    On    Error    00:00:24
gottcha-speDB-v    On    Error    00:00:01
gottcha2-speDB-v   On    Error    00:00:00
gottcha-strDB-b    On    Error    00:00:22
gottcha-strDB-v    On    Error    00:00:00
metaphlan2          On    Complete    00:02:03
bwa                     On    Complete    00:12:32
kraken                 On    Complete    00:00:50

---------------------------

I also see this in file: .../edge_ui/EDGE_output/./c63054c670d9aa8fa01abbb89f423134/error.log

   Segmentation fault (core dumped)
   No CDS annotation for phage finder
   convert-im6.q16: not authorized `/home/bee015guest/EdgeInstallDirectory/edge_dev/edge_ui/EDGE_output/c63054c670d9aa8fa01abbb89f423134/QcReads/QC_qc_report.pdf' @ error/constitute.c/ReadImage/412.
   convert-im6.q16: no images defined `/home/bee015guest/EdgeInstallDirectory/edge_dev/edge_ui/EDGE_output/c63054c670d9aa8fa01abbb89f423134/HTML_Report/images/QC_read_length.png' @ error/convert.c/ConvertImageCommand/3258.

./log/allReads-gottcha-strDB-b.log

 ...

---------------------------

I also see in edge_ui/EDGE_output/c63054c670d9aa8fa01abbb89f423134/ReadsBasedAnalysis/Taxonomy/log/allReads-gottcha-strDB-b.log (and the other related log files)

   ...

   [00:00:00] Mapping split-trimmed reads to GOTTCHA database and profiling...
   [00:00:22] ERROR: Failed running BWA or profileGottcha.pl. Please check /home/bee015guest/EdgeInstallDirectory/edge_dev/edge_ui/EDGE_output   /c63054c670d9aa8fa01abbb89f423134/ReadsBasedAnalysis/Taxonomy/1_allReads/gottcha-strDB-b/allReads.gottcha.log for detail.

The file mentioned, allReads.gottcha.log, does not exist.        

                                                                                                                   

---------------------------

Can anyone shed some light on what could be wrong? Or is it normal to get "Error" for those entries on the summary page?

Thank you

gmoore777

[gmoore777]

I've narrowed down the "Segmentation fault (core dumped)" message to this command:

+ profileGottcha.pl --parsedDB=/home/bee015guest/EdgeInstallDirectory/edge_dev/scripts/microbial_profiling/../../database/GOTTCHA/GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.genus.parsedGOTTCHA.dmp
--sam
--verbose
--outdir=/home/bee015guest/EdgeInstallDirectory/edge_dev/edge_ui/EDGE_output/4e319f9275a74f8e46a5bd48e014c9b7/ReadsBasedAnalysis/Taxonomy/1_allReads/gottcha-genDB-b/allReads_temp --prefix=allReads
--trimStats=/home/bee015guest/EdgeInstallDirectory/edge_dev/edge_ui/EDGE_output/4e319f9275a74f8e46a5bd48e014c9b7/ReadsBasedAnalysis/Taxonomy/1_allReads/gottcha-genDB-b/allReads_temp/allReads_splitrim.stats.txt
--treeFile=/home/bee015guest/EdgeInstallDirectory/edge_dev/scripts/microbial_profiling/../../database/GOTTCHA/speciesTreeGI.dmp
--genomeVitals=/home/bee015guest/EdgeInstallDirectory/edge_dev/scripts/microbial_profiling/../../database/GOTTCHA/genomeVitals.dmp
--noFastqOut
--method=1

I believe the `bwa` command prior to this was successful as I have redirected the output of `bwa` to a file, and that file

has 14689756 lines in it.

Running Ubuntu 18.04 with 8 CPUs and 32 GB memory.

Ran Edge with

         Input Source: NCBI SRA
         SRA Accession: SRX3660496

with "cpu=2", and with "cpu=4" and accepted all other defaults.

I really don't know if this error prevents me from doing something later on in the analysis

and I don't quite know how to divide and conquer any further than this, as I am very new to Edge and new to bioinformatics.

Was wondering if someone ran the same analysis, does it work for you?

Thank you

Gmoore777

[Lo, Chien-Chi]

Hi gmoore777,

 

EDGE release version doesn’t support Ubutnu 18.04 yet. Sorry about that but we are working on the Ubuntu 18.04 support. In the meantime, we encourage users to use Docker version of EDGE to get around the installation by providing a functioning EDGE full install on top of official CentOS Base Image (7.3.1611). 

 

For your question, I think you are right that the installation did not go well. You can check the install.log in the EDGE_HOME directory.  It looks like the split_trim program of the GOTTCHA tool doesn’t install/compile properly under the Ubuntu 18.04.  In addition, the image conversion needs to update its policy by the command below:

 

$ sed -i.bak 's/rights=\"none\" pattern=\"PDF\"/rights=\"read|write\" pattern=\"PDF\"/' /etc/ImageMagick-6/policy.xml

 

Best regards,

Chienchi

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[Greenleaf]

Hi Chienchi,

I think I solved the problems with the 6 gotcha- classifications failing
with:

    "Segmentation fault (core dumped)".


There is something funny going on with this line in
.../thirdParty/gottcha/bin/gottcha.pl

  $ENV{PERL5LIB} = "$RealBin/../ext/lib/perl5:$ENV{PERL5LIB}";


in conjunction with this line in thirdParty/gottcha/bin/profileGottcha.pl

  "use Storable;"


in conjunction with gottcha.pl calling profileGottcha.pl via a system()
command.


I replicated the above problem with 2 very small perl scripts.


Editing gottcha.pl and changing this line from:

  $ENV{PERL5LIB} = "$RealBin/../ext/lib/perl5:$ENV{PERL5LIB}";

To:

  $ENV{PERL5LIB} = "$ENV{PERL5LIB}";


Solved my problem.

[Lo, Chien-Chi]

Thanks.

I found the gottcha package come with compiled perl modules which doesn’t work on the newer Perl version. I will delete those pre-installed perl module and it will be fresh installed when EDGE ./INSTALL.sh be executed.

Thanks,
Chienchi