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.

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

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

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

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.