Partial run of the STAR-Fusion

[Panagiotis Papadopoulos]

Hello there,

It's been a while since I am trying to execute STAR-Fusion for my samples.  

The algorithm runs normally for some time, but then it stops with the following error. I can see some of the output files but not the most critical one related to the junctions. I need to say that I work in a cluster (so available RAM is not the case) and the IntervalTree.pm has been manually installed after my request. 

I would appreciate any help after all the troubleshooting. Thanks a lot!

Panagiotis

sample contains 55788674 rnaseq fragments
* Running CMD: /opt/bin/STAR-Fusion.v0.13.0/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /data/ppapadopoulos/ctat_genome_lib_build_dir  -J Chimeric.out.junction  -O /data/ppapadopoulos/StarFusionOut_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 48
Can't locate Set/IntervalTree.pm in @INC (you may need to install the Set::IntervalTree module) (@INC contains: /opt/bin/STAR-Fusion.v0.13.0/util/../PerlLib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.34.0 /usr/local/share/perl/5.34.0 /usr/lib/x86_64-linux-gnu/perl5/5.34 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.34 /usr/share/perl/5.34 /usr/local/lib/site_perl) at /opt/bin/STAR-Fusion.v0.13.0/util/STAR-Fusion.map_chimeric_reads_to_genes line 13.
BEGIN failed--compilation aborted at /opt/bin/STAR-Fusion.v0.13.0/util/STAR-Fusion.map_chimeric_reads_to_genes line 13.
Error, cmd: /opt/bin/STAR-Fusion.v0.13.0/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /data/ppapadopoulos/ctat_genome_lib_build_dir  -J Chimeric.out.junction  -O /data/ppapadopoulos/StarFusionOut_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 48  died with ret 512 No such file or directory at /opt/bin/STAR-Fusion.v0.13.0/PerlLib/Pipeliner.pm line 181.
Pipeliner::run(Pipeliner=HASH(0x56380ac36468)) called at /opt/bin/STAR-Fusion.v0.13.0/STAR-Fusion line 813

[Brian Haas]

Hi,

The main error here is: 

Can't locate Set/IntervalTree.pm in @INC (you may need to install the Set::IntervalTree module

You mentioned that it had been installed, but the system isn't finding it in any of the following locations:

(@INC contains: /opt/bin/STAR-Fusion.v0.13.0/util/../PerlLib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.34.0 /usr/local/share/perl/5.34.0 /usr/lib/x86_64-linux-gnu/perl5/5.34 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.34 /usr/share/perl/5.34 /usr/local/lib/site_perl) 

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas