Error when running Trinity

Question

[luzglongoria]

Hi there,

I have installed Trinity with conda but when I try to run it it gives me this error:

home/luz_garcia_longoria/miniconda3/pkgs/trinity-2.6.6-0/bin/Trinity --seqType fq --CPU 6 --max_memory 10G --single parasite_readsforTinity.fastq 2>&1 trinityparasite_noparasitenohost.log

which: no ParaFly in (/home/luz_garcia_longoria/miniconda3/pkgs/trinity-2.6.6-0/opt/trinity-2.6.6/trinity-plugins/BIN:/usr/lib64/qt-3.3/bin:/home/luz_garcia_longoria/perl5/bin:/var/bin/vcftools-vcftools-b240116/bin:/var/bin:/var/bin/trinityrnaseq-Trinity-v2.4.0:/var/bin/tophat-2.1.1.Linux_x86_64:/var/bin/stringtie-1.3.4d.Linux_x86_64:/var/bin/SPAdes-3.9.1-Linux/bin:/var/bin/IGVTools:/var/bin/seqtk-master:/var/bin/samtools-1.3.1:/var/bin/Salmon-0.8.2_linux_x86_64/bin:/var/bin/ribopicker-standalone-0.4.3:/var/bin/RAxML/:/var/bin/proteinortho_v5.11:/var/bin/PfamScan:/var/bin/paml4.8/bin:/var/bin/mothur/:/var/bin/KaKs_Calculator1.2/src:/var/bin/ima2-8.27.12/src/:/var/bin/IGVTools:/var/bin/IGV_2.3.44:/var/bin/hmmer-3.1b2-linux-intel-x86_64/binaries:/var/bin/hisat2-2.1.0:/var/bin/gff_scripts/:/var/bin/freebayes/bin:/var/bin/fastx:/var/bin/fastq_screen_v0.11.1:/var/bin/bowtie2-2.3.1:/var/bin/x86_64:/var/bin/x86_64-redhat-linux-gnu:/var/bin/mothur/blast/bin/:/var/bin/bedtools-2.17.0/bin:/var/bin/bcftools-1.4/:/var/bin/barrnap-master/bin:/var/bin/angsd/:/var/bin/ITSx_1.0.11:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/luz_garcia_longoria/.local/bin:/home/luz_garcia_longoria/bin)


Error, cannot locate Trinity-specific tool: ParaFly in the PATH setting: /home/luz_garcia_longoria/miniconda3/pkgs/trinity-2.6.6-0/opt/trinity-2.6.6/trinity-plugins/BIN:/usr/lib64/qt-3.3/bin:/home/luz_garcia_longoria/perl5/bin:/var/bin/vcftools-vcftools-b240116/bin:/var/bin:/var/bin/trinityrnaseq-Trinity-v2.4.0:/var/bin/tophat-2.1.1.Linux_x86_64:/var/bin/stringtie-1.3.4d.Linux_x86_64:/var/bin/SPAdes-3.9.1-Linux/bin:/var/bin/IGVTools:/var/bin/seqtk-master:/var/bin/samtools-1.3.1:/var/bin/Salmon-0.8.2_linux_x86_64/bin:/var/bin/ribopicker-standalone-0.4.3:/var/bin/RAxML/:/var/bin/proteinortho_v5.11:/var/bin/PfamScan:/var/bin/paml4.8/bin:/var/bin/mothur/:/var/bin/KaKs_Calculator1.2/src:/var/bin/ima2-8.27.12/src/:/var/bin/IGVTools:/var/bin/IGV_2.3.44:/var/bin/hmmer-3.1b2-linux-intel-x86_64/binaries:/var/bin/hisat2-2.1.0:/var/bin/gff_scripts/:/var/bin/freebayes/bin:/var/bin/fastx:/var/bin/fastq_screen_v0.11.1:/var/bin/bowtie2-2.3.1:/var/bin/x86_64:/var/bin/x86_64-redhat-linux-gnu:/var/bin/mothur/blast/bin/:/var/bin/bedtools-2.17.0/bin:/var/bin/bcftools-1.4/:/var/bin/barrnap-master/bin:/var/bin/angsd/:/var/bin/ITSx_1.0.11:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/luz_garcia_longoria/.local/bin:/home/luz_garcia_longoria/bin,  be sure to install Trinity by running 'make' in the base installation directory

If I go to the main directory of Trinity

cd home/luz_garcia_longoria/miniconda3/pkgs/trinity-2.6.6-0

Then I get this message

make: *** No targets specified and no makefile found.  Stop.

I installed Trinity by running this command:

conda install -c bioconda trinity

I don't know if something went wrong during the installation process. Can anyone help me, please?

[Ram]

Your error says "no ParaFly". Maybe try conda install -c bioconda parafly?

Answer 1

[h.mon]

I advise you to create an environment just for Trinity. Then install Trinity in this environment, and you should activate this environment to use Trinity:

conda create -n Trinity
conda activate Trinity
conda install -c bioconda trinity

If Parafly doesn't work on this environment, I would consider this a bug, you should open a ticket at bioconda.