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Old 01-19-2016, 01:14 AM   #1
Xiaopei
Junior Member
 
Location: Cambridge

Join Date: Jan 2016
Posts: 1
Post Trinity has "99.9997% completed" for 3 days.

Hi,

I am assembling about 540 million single RNA sequences with Trinity. I used normalized setting to finish it sooner.

The command I am using is: nice trinity2 --normalize_reads --seqType fq --single rnaseq_single_trimmed.fastq.gz --CPU 40 --max_memory 450G —verbose > & log &

In about 2 days, the status becomes:

---------------------------------------------------

----------- Chrysalis: QuantifyGraph --------------

-- (Integrate mapped reads into de Bruijn graph) --

---------------------------------------------------



* Running CMD: /biosoft/src/trinityrnaseq-2.1.1/trinity-plugins/parafly/bin/ParaFly -c /new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396551.trinity.reads.fa.out/chrysalis/quantifyGraph_commands -CPU 1 -failed_cmds failed_quantify_graph_commands.55174.txt -shuffle

* Running CMD: /biosoft/src/trinityrnaseq-2.1.1/Chrysalis/ReadsToTranscripts -i single.fa -f /new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396553.trinity.reads.fa.out/chrysalis/bundled_iworm_contigs.fasta -o /new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396553.trinity.reads.fa.out/chrysalis/readsToComponents.out -t 1 -max_mem_reads 50000000

succeeded(396550) 99.9987% completed. * Running CMD: /usr/bin/sort --parallel=1 -T . -S 1G -k 1,1n /new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396553.trinity.reads.fa.out/chrysalis/readsToComponents.out > /new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396553.trinity.reads.fa.out/chrysalis/readsToComponents.out.sort

CMD finished (0 seconds)

Butterfly_cmds: /new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396551.trinity.reads.fa.out/chrysalis/butterfly_commands

Fully cleaning up.

Inchworm and Chrysalis complete. Butterfly commands to execute are provided here:

/new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396551.trinity.reads.fa.out/chrysalis/butterfly_commands



---------------------------------------------------------------

-------------------- Butterfly --------------------------------

-- (Reconstruct transcripts from reads and de Bruijn graphs) --

---------------------------------------------------------------



* Running CMD: /biosoft/src/trinityrnaseq-2.1.1/trinity-plugins/parafly/bin/ParaFly -c /new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396551.trinity.reads.fa.out/chrysalis/butterfly_commands -shuffle -CPU 1 -failed_cmds failed_butterfly_commands.55174.txt

succeeded(396551) 99.999% completed. * Running CMD: /biosoft/src/trinityrnaseq-2.1.1/Inchworm/bin//FastaToDeBruijn --fasta /new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396553.trinity.reads.fa.out/chrysalis/bundled_iworm_contigs.fasta -K 24 --graph_per_record --threads 1 > /new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396553.trinity.reads.fa.out/chrysalis/bundled_iworm_contigs.fasta.deBruijn

* Running CMD: /biosoft/src/trinityrnaseq-2.1.1/util/support_scripts/partition_chrysalis_graphs_n_reads.pl --deBruijns /new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396553.trinity.reads.fa.out/chrysalis/bundled_iworm_contigs.fasta.deBruijn --componentReads /new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396553.trinity.reads.fa.out/chrysalis/readsToComponents.out.sort -N 1000 -L 200

CMD finished (0 seconds)

Fully cleaning up.

succeeded(396552) 99.9992% completed. ---------------------------------------------------

----------- Chrysalis: QuantifyGraph --------------

-- (Integrate mapped reads into de Bruijn graph) --

---------------------------------------------------



* Running CMD: /biosoft/src/trinityrnaseq-2.1.1/trinity-plugins/parafly/bin/ParaFly -c /new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396553.trinity.reads.fa.out/chrysalis/quantifyGraph_commands -CPU 1 -failed_cmds failed_quantify_graph_commands.55278.txt -shuffle

Butterfly_cmds: /new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396553.trinity.reads.fa.out/chrysalis/butterfly_commands

Inchworm and Chrysalis complete. Butterfly commands to execute are provided here:

/new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396553.trinity.reads.fa.out/chrysalis/butterfly_commands



---------------------------------------------------------------

-------------------- Butterfly --------------------------------

-- (Reconstruct transcripts from reads and de Bruijn graphs) --

---------------------------------------------------------------



* Running CMD: /biosoft/src/trinityrnaseq-2.1.1/trinity-plugins/parafly/bin/ParaFly -c /new-data/xs253/trinity_out_dir/read_partitions/Fb_3/CBin_3965/c396553.trinity.reads.fa.out/chrysalis/butterfly_commands -shuffle -CPU 1 -failed_cmds failed_butterfly_commands.55278.txt

CMD finished (0 seconds)

Fully cleaning up.

succeeded(396553) 99.9995% completed. CMD finished (0 seconds)

Fully cleaning up.

succeeded(396554) 99.9997% completed.



It looks fine but it has been like this for 3 days, without a little change at all. It is not finished, as the final Trinity.fasta is not generated. I am not sure what should I do next. Should I restart it?

Any advice will be very appreciated!
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