Hi
I want to de-novo assemble 60 million PE RNA-seq reads with Trinity (with ActivePerl installation in my home directory). I tried it two times but Trinity does not finish.
The command was:
nohup Trinity --seqType fq --max_memory 80G --left H2_rnaseq_R1_trimmed.fastq.gz --right H2_rnaseq_R2_trimmed.fastq.gz --CPU 10 --jaccard_clip &
Trinity starts just fine and runs for several hours writing around 44GB of intermediate results to disk. After that Trinity stops and the last entry from nohup.out is:
The file "FailedCommands" just states:
Any advice is welcome. Thanks in advance!
I want to de-novo assemble 60 million PE RNA-seq reads with Trinity (with ActivePerl installation in my home directory). I tried it two times but Trinity does not finish.
The command was:
nohup Trinity --seqType fq --max_memory 80G --left H2_rnaseq_R1_trimmed.fastq.gz --right H2_rnaseq_R2_trimmed.fastq.gz --CPU 10 --jaccard_clip &
Trinity starts just fine and runs for several hours writing around 44GB of intermediate results to disk. After that Trinity stops and the last entry from nohup.out is:
---------------------------------------------------------------
-------------------- Butterfly --------------------------------
-- (Reconstruct transcripts from reads and de Bruijn graphs) --
---------------------------------------------------------------
Butterfly_cmds: /scratchsan/kai/rnaseq/trinity_out_dir/read_partitions/Fb_0/CBin_0/c27478.trinity.reads.fa.out/chrysalis/butterfly_commands
Inchworm and Chrysalis complete. Butterfly commands to execute are provided here:
/scratchsan/kai/rnaseq/trinity_out_dir/read_partitions/Fb_0/CBin_0/c27478.trinity.reads.fa.out/chrysalis/butterfly_commands
Thursday, February 12, 2015: 02:50:35 CMD: /homes/biertank/kai/software/trinityrnaseq-2.0.2/trinity-plugins/parafly/bin/ParaFly -c /scratchsan/kai/rnaseq/trinity_out_dir/read_partitions/Fb_0/CBin_0/c27478.trinity.reads.fa.out/chrysalis/butterfly_commands -shuffle -CPU 1 -failed_cmds failed_butterfly_commands.41256.txt -v
Number of Commands: 1
succeeded(1) 100% completed.
All commands completed successfully. :-)
CMD finished (0 seconds)
Thursday, February 12, 2015: 02:50:35 CMD: /homes/biertank/kai/software/trinityrnaseq-2.0.2/util/support_scripts/print_butterfly_assemblies.pl /scratchsan/kai/rnaseq/trinity_out_dir/read_partitions/Fb_0/CBin_0/c27478.trinity.reads.fa.out/chrysalis/component_base_listing.txt > Trinity.fasta.tmp
CMD finished (0 seconds)
Fully cleaning up.
###################################################################
Butterfly assemblies are written to /scratchsan/kai/rnaseq/trinity_out_dir/read_partitions/Fb_0/CBin_0/c27478.trinity.reads.fa.out.Trinity.fasta
###################################################################
succeeded(27478), failed(1) 100% completed.
We are sorry, commands in file: [FailedCommands] failed. :-(
Error, cmd: /homes/biertank/kai/software/trinityrnaseq-2.0.2/trinity-plugins/parafly/bin/ParaFly -c recursive_trinity.cmds -CPU 10 -v died with ret 256 at /homes/biertank/kai/software/trinityrnaseq-2.0.2/Trinity line 1997.
Trinity run failed. Must investigate error above. at /homes/biertank/kai/software/trinityrnaseq-2.0.2/Trinity line 1057.
-------------------- Butterfly --------------------------------
-- (Reconstruct transcripts from reads and de Bruijn graphs) --
---------------------------------------------------------------
Butterfly_cmds: /scratchsan/kai/rnaseq/trinity_out_dir/read_partitions/Fb_0/CBin_0/c27478.trinity.reads.fa.out/chrysalis/butterfly_commands
Inchworm and Chrysalis complete. Butterfly commands to execute are provided here:
/scratchsan/kai/rnaseq/trinity_out_dir/read_partitions/Fb_0/CBin_0/c27478.trinity.reads.fa.out/chrysalis/butterfly_commands
Thursday, February 12, 2015: 02:50:35 CMD: /homes/biertank/kai/software/trinityrnaseq-2.0.2/trinity-plugins/parafly/bin/ParaFly -c /scratchsan/kai/rnaseq/trinity_out_dir/read_partitions/Fb_0/CBin_0/c27478.trinity.reads.fa.out/chrysalis/butterfly_commands -shuffle -CPU 1 -failed_cmds failed_butterfly_commands.41256.txt -v
Number of Commands: 1
succeeded(1) 100% completed.
All commands completed successfully. :-)
CMD finished (0 seconds)
Thursday, February 12, 2015: 02:50:35 CMD: /homes/biertank/kai/software/trinityrnaseq-2.0.2/util/support_scripts/print_butterfly_assemblies.pl /scratchsan/kai/rnaseq/trinity_out_dir/read_partitions/Fb_0/CBin_0/c27478.trinity.reads.fa.out/chrysalis/component_base_listing.txt > Trinity.fasta.tmp
CMD finished (0 seconds)
Fully cleaning up.
###################################################################
Butterfly assemblies are written to /scratchsan/kai/rnaseq/trinity_out_dir/read_partitions/Fb_0/CBin_0/c27478.trinity.reads.fa.out.Trinity.fasta
###################################################################
succeeded(27478), failed(1) 100% completed.
We are sorry, commands in file: [FailedCommands] failed. :-(
Error, cmd: /homes/biertank/kai/software/trinityrnaseq-2.0.2/trinity-plugins/parafly/bin/ParaFly -c recursive_trinity.cmds -CPU 10 -v died with ret 256 at /homes/biertank/kai/software/trinityrnaseq-2.0.2/Trinity line 1997.
Trinity run failed. Must investigate error above. at /homes/biertank/kai/software/trinityrnaseq-2.0.2/Trinity line 1057.
/homes/biertank/kai/software/trinityrnaseq-2.0.2/util/support_scripts/../../Trinity --single "/scratchsan/kai/rnaseq/trinity_out_dir/read_partitions/Fb_0/CBin_0/c9162.trinity.reads.fa" --output "/scratchsan/kai/rnaseq/trinity_out_dir/read_partitions/Fb_0/CBin_0/c9162.trinity.reads.fa.out" --CPU 1 --max_memory 1G --full_cleanup --seqType fa --trinity_complete --jaccard_clip
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