error running star-fusion

[Fernando Jimenez]

Hi!

I installed STAR-fusion through Anaconda, and downloaded the CTAT genome from:

https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play.tar.gz

After untar the lib I executed STAR-fusion under its conda env with 2 fastq PE with 30 threads to check if it works. But I get the following error:

CMD: mkdir -p /home/laboratorio/Fer/fusion_alex/STAR-fusion/star_fusion_outdir/_starF_checkpoints
CMD: mkdir -p /home/laboratorio/Fer/fusion_alex/STAR-fusion/star_fusion_outdir/star-fusion.preliminary
* Running CMD: /home/Aplicaciones/anaconda3/envs/starfusion/bin/STAR --genomeDir /home/laboratorio/Fer/fusion_alex/STAR-fusion/ctat_data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx  --outReadsUnmapped None  --chimSegmentMin 12  --chimJunctionOverhangMin 12  --chimOutJunctionFormat 1  --alignSJDBoverhangMin 10  --alignMatesGapMax 100000  --alignIntronMax 100000  --alignSJstitchMismatchNmax 5 -1 5 5  --runThreadN 30 --outSAMstrandField intronMotif  --outSAMunmapped Within  --outSAMtype BAM Unsorted  --readFilesIn /home/laboratorio/Fer/fusion_alex/STAR-fusion/./fastq_trimmed/PDAC_001_CTGAAGCT-GTACTGAC_L004_R1_001_val_1.fq.gz /home/laboratorio/Fer/fusion_alex/STAR-fusion/./fastq_trimmed/PDAC_001_CTGAAGCT-GTACTGAC_L004_R2_001_val_2.fq.gz  --outSAMattrRGline ID:GRPundef  --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10  --peOverlapNbasesMin 12 --peOverlapMMp 0.1  --genomeLoad NoSharedMemory  --twopassMode Basic  --readFilesCommand 'gunzip -c'
Mar 17 09:46:38 ..... started STAR run
Mar 17 09:46:38 ..... loading genome
Mar 17 09:46:55 ..... started 1st pass mapping
Mar 17 09:48:30 ..... finished 1st pass mapping
Mar 17 09:48:31 ..... inserting junctions into the genome indices
Mar 17 09:50:12 ..... started mapping
Mar 17 09:53:28 ..... finished mapping
Mar 17 09:53:32 ..... finished successfully
-sample contains 18902737
* Running CMD: /home/Aplicaciones/anaconda3/envs/starfusion/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /home/laboratorio/Fer/fusion_alex/STAR-fusion/ctat_data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir  -J Chimeric.out.junction  > /home/laboratorio/Fer/fusion_alex/STAR-fusion/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt
-building interval tree based on /home/laboratorio/Fer/fusion_alex/STAR-fusion/ctat_data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.05 min).
-parsing fusion evidence: Chimeric.out.junction
-mapping reads to genes
Argument "brkpt_donorA" isn't numeric in preincrement (++) at /home/Aplicaciones/anaconda3/envs/starfusion/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes line 379, <$fh> line 1.
Can't use an undefined value as an ARRAY reference at /home/Aplicaciones/anaconda3/envs/starfusion/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes line 511, <$fh> line 1.
Error, cmd: /home/Aplicaciones/anaconda3/envs/starfusion/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /home/laboratorio/Fer/fusion_alex/STAR-fusion/ctat_data/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir  -J Chimeric.out.junction  > /home/laboratorio/Fer/fusion_alex/STAR-fusion/star_fusion_outdir/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt died with ret 6400 No such file or directory at /home/Aplicaciones/anaconda3/envs/starfusion/lib/STAR-Fusion/PerlLib/Pipeliner.pm line 181.
    Pipeliner::run(Pipeliner=HASH(0x55622ebd0e00)) called at /home/Aplicaciones/anaconda3/envs/starfusion/lib/STAR-Fusion/STAR-Fusion line 678

I would appreciate any help with this,

Kind regards,

[Brian Haas]

hi,

I'm not sure what's going on with the conda release, but others in the community build the conda release so they might look into it.

You can pull our latest code here:  https://github.com/STAR-Fusion/STAR-Fusion/releases/download/v1.10.0/STAR-Fusion-v1.10.0.FULL.tar.gz

Just untar it, run 'make' in the base directory, and you should be good to go.  If it continues to cause trouble, let me know.

best,

~b

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Brian J. Haas
The Broad Institute
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[Fernando Jimenez]

Thank you Brian!

I pulled the last code as you suggested and it worked (using STAR in a conda env and calling it with > perl STAR-Fusion ...). I will try now with the full dataset... fingers crossed! (if something happens I text here again:) )

Lets see if someone can find the solution to the conda release,..., but in this way is working perfectly.

Thank you for your help!

Kindest regards,

Fer

[Brian Haas]

terrific!  great to hear.

I'd like to support conda too, but there's not enough time in the day to do everything with minimal resources.

best,

~b

To view this discussion on the web visit https://groups.google.com/d/msgid/star-fusion/f0e003dc-c0c9-4d37-bef0-632a3a051d02n%40googlegroups.com.

[Fernando Jimenez]

hehehe fair enough Brian... It works nicely. Conda guys will check it at some point (maybe is something in my system...) XD

Thanks a lot!

best,

Fer