Index of /examples/bioinformatics/trinity

Icon  Name                    Last modified      Size  Description
[DIR] Parent Directory - [   ] reads.left.fq.gz 01-Oct-2016 22:43 1.2M [   ] reads.right.fq.gz 01-Oct-2016 22:43 1.2M [   ] reads2.left.fq.gz 01-Oct-2016 22:43 1.2M [   ] reads2.right.fq.gz 01-Oct-2016 22:43 1.2M [   ] scc.conf 01-Oct-2016 23:25 644 [   ] reads.right.fqi 01-Oct-2016 23:28 5.6M [   ] trinity.qsub 01-Oct-2016 23:33 498

Trinity


Interactive Usage:

# Load Modules

[scc4]$ module load bowtie/1.1.2
[scc4]$ module load trinity/2.2.0

# Prepare the Data

[scc4]$ gunzip -c reads.right.fq.gz > reads.right.fqi
[scc4]$ gunzip -c reads.left.fq.gz > reads.left.fq
[scc4]$ gunzip -c reads2.right.fq.gz > reads2.right.fq
[scc4]$ gunzip -c reads2.left.fq.gz > reads2.left.fq


# Assemble RNA-Seq data:

[scc4]$ Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 1 --no_cleanup --normalize_reads

Trinity version: v2.2.0
-currently using the latest production release of Trinity.

* Found ParaFly installed at: /share/pkg/trinity/2.2.0/install/trinity-plugins/parafly/bin/ParaFly

Saturday, October 1, 2016: 22:57:39 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /share/pkg/trinity/2.2.0/install/util/support_scripts/ExitTester.jar 0
Saturday, October 1, 2016: 22:57:39 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /share/pkg/trinity/2.2.0/install/util/support_scripts/ExitTester.jar 1


----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
----------------------------------------------------------------------------------

---------------------------------------------------------------
------------ In silico Read Normalization ---------------------
-- (Removing Excess Reads Beyond 50 Coverage --
-- /project/scv/examples/bioinformatics/trinity/trinity_out_dir/insilico_read_normalization --
---------------------------------------------------------------


#######################################################################
Inchworm file: /project/scv/examples/bioinformatics/trinity/trinity_out_dir/inchworm.K25.L25.fa detected.
Skipping Inchworm Step, Using Previous Inchworm Assembly
#######################################################################

-- Skipping CMD: /share/pkg/trinity/2.2.0/install/util/misc/fasta_filter_by_min_length.pl /project/scv/examples/bioinformatics/trinity/trinity_out_dir/inchworm.K25.L25.fa 100 > /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100, checkpoint exists.
-- Skipping CMD: bowtie-build -q /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100, checkpoint exists.
-- Skipping CMD: bash -c " set -o pipefail; bowtie -a -m 20 --best --strata --threads 4 --chunkmbs 512 -q -S -f /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 both.fa | samtools view -@ 4 -F4 -Sb - | samtools sort -m 268435456 -@ 4 -no - - > /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" , checkpoint exists.
-- Skipping CMD: /share/pkg/trinity/2.2.0/install/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /project/scv/examples/bioinformatics/trinity/trinity_out_dir/inchworm.K25.L25.fa > /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/iworm_scaffolds.txt, checkpoint exists.
-- Skipping CMD: /share/pkg/trinity/2.2.0/install/Chrysalis/GraphFromFasta -i /project/scv/examples/bioinformatics/trinity/trinity_out_dir/inchworm.K25.L25.fa -r both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 4 -k 24 -kk 48 -strand -scaffolding /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/iworm_scaffolds.txt > /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/GraphFromIwormFasta.out, checkpoint exists.
-- Skipping CMD: /share/pkg/trinity/2.2.0/install/Chrysalis/CreateIwormFastaBundle -i /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200, checkpoint exists.
-- Skipping CMD: /share/pkg/trinity/2.2.0/install/Chrysalis/ReadsToTranscripts -i both.fa -f /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/readsToComponents.out -t 4 -max_mem_reads 50000000 -strand , checkpoint exists.
-- Skipping CMD: /bin/sort -T . -S 2G -k 1,1n /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/readsToComponents.out > /project/scv/examples/bioinformatics/trinity/trinity_out_dir/chrysalis/readsToComponents.out.sort, checkpoint exists.


--------------------------------------------------------------------------------
------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
--------------------------------------------------------------------------------

$VAR1 = {
'grid' => 'SGE',
'cmd' => 'qsub -V -cwd -P krcs',
'max_nodes' => '10',
'cmds_per_node' => '1'
};
CMDS: 9 / 82 [9/10 nodes in use]
CMDS: 82 / 82 [2/10 nodes in use]
* All cmds submitted to grid. Now waiting for them to finish.
CMDS: 82 / 82 [0/10 nodes in use]
* All nodes completed. Now auditing job completion status values
All commands completed successfully.
Finished.

All commands completed successfully on the computing grid.


** Harvesting all assembled transcripts into a single multi-fasta file...

Saturday, October 1, 2016: 23:02:20 CMD: find read_partitions/ -name '*inity.fasta' | /share/pkg/trinity/2.2.0/install/util/support_scripts/partitioned_trinity_aggregator.pl TRINITY_DN > Trinity.fasta.tmp


###################################################################
Butterfly assemblies are written to /project/scv/examples/bioinformatics/trinity/trinity_out_dir/Trinity.fasta
###################################################################




Batch Usage:


scc4% qsub -P {project} trinity.qsub


Documentation: