trinitry Virusfinder error message no contigs

Question

[cristina_sabiers]

well Im spending all morning installing all the programs and config what virusfinder needs... I get this message ;____; any clue? I reinstalled trinity like three time and always tells everything is installed right.

perl VirusFinder.pl -c config.txt

mar sep 27 19:01:33 CEST 2016

step 1 preprocessing...

awk: line 2: function and never defined

step 2 detect virus..
.
step 2.1 map reads to virus database...

step 2.2 garner reads mapped to the virus database...

step 2.3 de novo assembly using Trinity...

Uncaught exception from user code:

    Error: Trinity did not output contigs. Please make sure Trinity works.


Failed to detect viruses.

any help will be appreciate to my poor burned brain....

Thanks!!!

[Farbod]

Dear cristina_sabiers, Hi

I dont think that the VirusFinder is embedded in Trinity assembler software as I have used version 2.2 of it and I did not heard about that and even there is no question in this regard in Trinity group.

So, if you put all the needed programs correctly in your PATH, I suggest that ask your question from Trinity Group which is a very active and strong group.

In addition, maybe this article can helps you. search for the "Configuration file" section, please.

Hope that helps.

[cristina_sabiers]

Thanks

Tomorrow I will check once again and reinstall all, if isnt working will post help in the trinity group...Im a newbee so can be I do something wrong.

[Farbod]

It is not really a Trinity issue but may be they can help.

[GenoMax]

I don't see a virus finder in trinity either so am not sure where you are getting that from.

[GenoMax]

What Trinity package is this?

[cristina_sabiers]

trinityrnaseq_2.2.0 :)

[GenoMax]

Is this the test data going through or your own?

[cristina_sabiers]

I use my own fastq and bam files if is that what you mean :)

I tried with simulation data and results is the same

Answer 1

[harips619]

I found a solution for this error. Install Trinity 2.5.1 in latest ubuntu. Run Trinity on test files to check whether Trinity installed correctly. Then change `perl $ILIBs $trinity_script --seqType fa --JM 4G --single blat_out_candidate_singlelane.fa --min_contig_length $min_contig_length --output trinity_output --CPU $thread_no --bfly_opts \"-V 10 --stderr\"; to perl $ILIBs $trinity_script --seqType fa --max_memory 50G --single blat_out_candidate_singlelane.fa --min_contig_length $min_contig_length --output trinity_output; in detect_virus.pl. After that it works with unmapped fastq files.

Answer 2

[cristina_sabiers]

I posted for help in the group, hope someone can help me....Im wondering if I do something wrong in the config file?Thanks

I use the fastq file and bam file from the same person (Im bit confuse in that point if is right)

alignment_file = /media/cri/CRIS_DATA/VIRUSFINDER/FASTQ/02.bam

fastq1 = /media/cri/CRIS_DATA/VIRUSFINDER/seq_1.fastq.gz

mailto = [e-mail] thread_no = 8

detect_integration = yes # if no is provided, VirusFinder will not detect virus integrations

detect_mutation = yes # if no is provided, VirusFinder will not detect viral mutations

<h6>#</h6>

The full paths to the following third-party tools are required by VirusFinder:

<h6>#</h6>

blastn_bin = /home/cri/Desktop/ncbi-blast-2.5.0+/blastn

bowtie_bin = /media/cri/CRIS_DATA/VIRUSFINDER/bowtie2-2.2.9/bowtie2

bwa_bin = /media/cri/CRIS_DATA/VIRUSFINDER/bwa.kit/bwa

trinity_script = /home/cri/Desktop/trinityrnaseq-2.2.0/Trinity.pl

SVDetect_dir = /media/cri/CRIS_DATA/VIRUSFINDER/SVDetect_r0.8b

<h6>#</h6>

Reference files indexed for Bowtie2 and BLAST

<h6>#</h6>

bowtie_index_human = /media/cri/CRIS_DATA/VIRUSFINDER/VirusFinder2.0/bw/hg19

blastn_index_human = /media/cri/CRIS_DATA/VIRUSFINDER/VirusFinder2.0/blast/hg19

<h6>#</h6>

Parameters of virus integration detection. They are ignored for single-end data

<h6>#</h6>

detection_mode = sensitive

flank_region_size = 4000

sensitivity_level = 1

<h6>#</h6>

Parameters of virus detection. Smaller “min_contig_length”, higher sensitivity

<h6>#</h6>

min_contig_length = 300

blastn_evalue_thrd = 0.05

similarity_thrd = 0.8

chop_read_length = 25

minIdentity = 80

[GenoMax]

@cristina: This is not part of Trinity, AFAIK. You are running this tool independently correct?

[cristina_sabiers]

this is the config.txt from virusfinder, I only change all of that following manual and after I write:

perl VirusFinder.pl -c config.txt

I dont do anything else

[GenoMax]

Sorry to be pedantic but how is trinity RNAseq assembler related to this question (since you have it in the title)?

[cristina_sabiers]

Because when I write perl VirusFinder.pl -c config.txt

I get this error message :) I thought was st wrong with it:

step 2.3 de novo assembly using Trinity...

Uncaught exception from user code:

Error: Trinity did not output contigs. Please make sure Trinity works.

[GenoMax]

This sounds like you are using an application called VirusFinder that calls Trinity externally and that part is failing.

First thing to check would be a need for a specific version of Trinity as far as VirusFinder is concerned. Perhaps it does not work with the latest Trinity.

[cristina_sabiers]

ok! thanks! I will check out tomorrow ^^

[Farbod]

Hi, have you check if Trinity and its plugins are ready to use (using make & make plugins command) and have you test it by sample data which Trinity has provided to check if it really work?

cd sample_data/test_Trinity_Assembly/

./runMe.sh

And do you put Bowtie and Trinity in your Linux PATH as the VirusFinder has proposed in its configuration file?

[cristina_sabiers]

I have done now with the newst version from trinity

succeeded(86) 100% completed.

All commands completed successfully. :-)

[cristina_sabiers]

I was checking on the manual, is stands trinity version 2012_06_08 so I download it and tried to install, I get this error message

g++  -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels  -O3  -ggdb3 -DMAKE_DATE='"jue sep 29 17:00:27 CEST 2016"' -DMAKE_OS_RELEASE='"4.4.0-38-generic"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread  -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp   -fopenmp       -c ./aligns/KmerAlignCore.cc -o obj/aligns/KmerAlignCore.o
./aligns/KmerAlignCore.cc:6:34: fatal error: aligns/KmerAlignCore.h: No such file or directory
compilation terminated.
Makefile:465: recipe for target 'aligns/KmerAlignCore.o' failed

what does it means?

[GenoMax]

A version from 2012? That sounds a bit hopeless. Check with VirusFinder authors to see if you can use a newer version of Trinity or directly jump to the step after trinity (if you have contigs from Trinity already available).

Error is clear though: aligns/KmerAlignCore.h: No such file or directory

[cristina_sabiers]

yes, but the most space thing the folder are there and also that kmeraligncore I found this looks someone got something similar and is because gcc5 compatibility (If i understand right, Im not informatic)

https://github.com/trinityrnaseq/trinityrnaseq/issues/47

I had take contact with Virusfinder author, hope they can help me

Answer 3

[cristina_sabiers]

well I talked with the developers of Virusfinder... it only works with trinityversion 2012 which I cant install in my ubuntu 16 LTS.

Any ideas how I can fix this issue? I try to do the steps manually in the last version from Trinity but I must say I am bit losted

I get stopped by virus finder on step 2.3, which the code is.

print "step 2.3 de novo assembly using Trinity...\n";

my $updated = 0;

if (!-e 'Trinity-init.fasta'){
$updated = 1;

my $ILIBs = GetIdir();
`perl $ILIBs $trinity_script --seqType fa  --JM 4G --single blat_out_candidate_singlelane.fa --min_contig_length $min_contig_length  --output trinity_output --CPU $thread_no --bfly_opts \"-V 10 --stderr\"`;

if (-e 'trinity_output/Trinity.fasta' && -s 'trinity_output/Trinity.fasta'){
    print "Finished read assembly\n";
}else{
    if (!-e 'trinity_output'){
        die "\nError: Trinity did not output contigs. Please make sure Trinity works.\n\n";
    }else{
        `rm -r trinity_output`;

        print "\nWarning: Trinity did not output contigs (min contig length=$min_contig_length)!\n\n";

        my $contig_len = $min_contig_length >> 1;
        my $read1_len  = `sed '2q;d' unmapped.1.fa | awk '\{print length(\$0)\}'`;
        chomp $read1_len;
        $contig_len = ($min_contig_length + $read1_len) >> 1 if ($contig_len <= $read1_len);

        print "\nRetry Trinity using a shorter contig length $contig_len...\n\n";

        `perl $ILIBs $trinity_script --seqType fa  --JM 4G --single blat_out_candidate_singlelane.fa --min_contig_length $contig_len  --output trinity_output --CPU $thread_no --bfly_opts \"-V 10 --stderr\"`;

    if (!-e 'trinity_output/Trinity.fasta' || !-s 'trinity_output/Trinity.fasta'){
            `rm -r trinity_output`;
            die "\nError: Trinity did not output contigs!\n\n";
        }else{
        print "Finished read assembly\n";
        }
    }
}

`mv trinity_output/Trinity.fasta Trinity-init.fasta`;
`rm -r trinity_output`;
 }

`if ($updated || !-e 'Trinity.fasta'){
$updated = 1;
print "Discard low complexity contigs...\n";
ReformatOutput('Trinity-init.fasta', 'Trinity.fasta', $dust_cutoff);
}

if ($updated || !-e 'clean_blastn.fa'){
$updated = 1;
print "blastn contigs against human genome...\n";
`$blastn_bin -query=Trinity.fasta -db=$blastn_index_human -evalue $blastn_evalue_thrd -outfmt 6 > human_contig.txt`;

print "clean up blastn outputs\n";
BlastnCleanup('human_contig.txt', 'Trinity.fasta', 'clean_blastn.fa', $similarity_thrd);   #pull out non-human contig into clean_blastn.fa

So I copied the file blat_out_candidate_singlelane.fa and others to trinity folder and I write this code

perl Trinity --seqType fa  --max_memory 32G  --single blat_out_candidate_singlelane.fa --min_contig_length 300  --output trinity_output --CPU 4

but I get this error message

    usage: /media/cri/CRIS_DATA/trinityrnaseq-2.2.0/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file <string> [Trinity params]
  #
  # Required:
  #
  # --reads_list_file <string>      file containing list of filenames corresponding 
  #                                                  to the reads.fasta

which file is suposse to be this --reads_list_file ??

Thanks...hope what I am doing isnt crazy

[Ron]

Were you able to find the older version of Trinity?

Answer 4

[efratdahan21]

hi cristina sabiers ! i had exactly the same problem with trinity and virus finder!! did you succeed to run trinity in new version from the output of step 2 of virusfinder2 before it failed? ill be happy to discuss with you about you if you have some ideas for me thanks in advance, Efrat

Answer 5

[fx32]

I got the same issue before, but made it work through this version of Trinity: trinityrnaseq_r2012-06-08.tgz https://sourceforge.net/projects/trinityrnaseq/files/PREV_CONTENTS/previous_releases/

Hope it help for future users.

[bioinfo89]

Hi @fx32,

I am also facing the same issue for trinity. I installed trinity version which you have shared above, but i still get the same error.

[Peng Huang]

I did the same thing and still get the same error, but I found it might due to the too high value of "thread_no" setted in the configure file. (actually, for sample input, it works at 8 threads but failed at 32 threads)