trinitry Virusfinder error message no contigs
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6.2 years ago

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!!!

virus • 3.8k views
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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.

Hope that helps.

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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.

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

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

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What Trinity package is this?

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trinityrnaseq_2.2.0 :)

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Is this the test data going through or your own?

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

I tried with simulation data and results is the same

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4.7 years ago
harips619 ▴ 10

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. ADD COMMENT 0 Entering edit mode 6.2 years ago 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 = xxx@hotmail.com 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 ADD COMMENT 0 Entering edit mode @cristina: This is not part of Trinity, AFAIK. You are running this tool independently correct? ADD REPLY 0 Entering edit mode 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 ADD REPLY 1 Entering edit mode Sorry to be pedantic but how is trinity RNAseq assembler related to this question (since you have it in the title)? ADD REPLY 0 Entering edit mode 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. ADD REPLY 1 Entering edit mode 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. ADD REPLY 0 Entering edit mode ok! thanks! I will check out tomorrow ^^ ADD REPLY 1 Entering edit mode 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? ADD REPLY 0 Entering edit mode I have done now with the newst version from trinity succeeded(86) 100% completed. All commands completed successfully. :-) ADD REPLY 0 Entering edit mode 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? ADD REPLY 0 Entering edit mode 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 ADD REPLY 0 Entering edit mode 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 ADD REPLY 0 Entering edit mode 6.2 years ago 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"; myupdated = 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'){
}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{
}
}
}

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

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

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

Thanks...hope what I am doing isnt crazy

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Were you able to find the older version of Trinity?

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5.7 years ago

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

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5.2 years ago
fx32 • 0

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.

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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.

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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)