STAR-Fusion error

[takeshi kobayashi]

I am having trouble running the software and facing the error below. Can you please provide me with a solution? 

STAR-Fusion --left_fq SRR15343251_1.fastq  --right_fq SRR15343251_2.fastq --genome_lib_dir /home/ha7785/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir --CPU 4 --output_dir star_fusion_SRR15343251
CMD: mkdir -p /rshare1/ZETTAI_path_WA_slash_home_KARA/home/ha7785/star_fusion_SRR15343251
CMD: mkdir -p /rshare1/ZETTAI_path_WA_slash_home_KARA/home/ha7785/star_fusion_SRR15343251/_starF_checkpoints
CMD: mkdir -p /rshare1/ZETTAI_path_WA_slash_home_KARA/home/ha7785/star_fusion_SRR15343251/star-fusion.preliminary
* Running CMD: /home/ha7785/miniconda3/envs/aligners/bin/STAR --genomeDir /home/ha7785/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 4 --outSAMstrandField intronMotif  --outSAMunmapped Within  --outSAMtype BAM Unsorted  --readFilesIn /rshare1/ZETTAI_path_WA_slash_home_KARA/home/ha7785/SRR15343251_1.fastq /rshare1/ZETTAI_path_WA_slash_home_KARA/home/ha7785/SRR15343251_2.fastq  --outSAMattrRGline ID:GRPundef  --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10  --peOverlapNbasesMin 12 --peOverlapMMp 0.1  --genomeLoad NoSharedMemory  --twopassMode Basic
        /home/ha7785/miniconda3/envs/aligners/bin/STAR --genomeDir /home/ha7785/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 4 --outSAMstrandField intronMotif --outSAMunmapped Within --outSAMtype BAM Unsorted --readFilesIn /rshare1/ZETTAI_path_WA_slash_home_KARA/home/ha7785/SRR15343251_1.fastq /rshare1/ZETTAI_path_WA_slash_home_KARA/home/ha7785/SRR15343251_2.fastq --outSAMattrRGline ID:GRPundef --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --genomeLoad NoSharedMemory --twopassMode Basic
        STAR version: 2.7.10b   compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
Dec 17 07:00:43 ..... started STAR run
Dec 17 07:00:43 ..... loading genome
Dec 17 07:01:14 ..... started 1st pass mapping
Dec 17 08:06:00 ..... finished 1st pass mapping
Dec 17 08:06:01 ..... inserting junctions into the genome indices
Dec 17 08:08:33 ..... started mapping
Dec 17 09:32:45 ..... finished mapping
Dec 17 09:32:48 ..... finished successfully
-sample contains 64309159
* Running CMD: /rshare1/ZETTAI_path_WA_slash_home_KARA/home/ha7785/miniconda3/envs/aligners/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /home/ha7785/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir  -J Chimeric.out.junction  > /rshare1/ZETTAI_path_WA_slash_home_KARA/home/ha7785/star_fusion_SRR15343251/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt
-building interval tree based on /home/ha7785/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.20 min).
-parsing fusion evidence: Chimeric.out.junction
-mapping reads to genes
Argument "brkpt_donorA" isn't numeric in preincrement (++) at /rshare1/ZETTAI_path_WA_slash_home_KARA/home/ha7785/miniconda3/envs/aligners/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes line 379, <$fh> line 1.
Can't use an undefined value as an ARRAY reference at /rshare1/ZETTAI_path_WA_slash_home_KARA/home/ha7785/miniconda3/envs/aligners/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes line 511, <$fh> line 1.
Error, cmd: /rshare1/ZETTAI_path_WA_slash_home_KARA/home/ha7785/miniconda3/envs/aligners/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /home/ha7785/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir  -J Chimeric.out.junction  > /rshare1/ZETTAI_path_WA_slash_home_KARA/home/ha7785/star_fusion_SRR15343251/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt died with ret 6400 No such file or directory at /rshare1/ZETTAI_path_WA_slash_home_KARA/home/ha7785/miniconda3/envs/aligners/lib/STAR-Fusion/PerlLib/Pipeliner.pm line 181.
        Pipeliner::run(Pipeliner=HASH(0x5560750b23d0)) called at /home/ha7785/miniconda3/envs/aligners/lib/STAR-Fusion/STAR-Fusion line 678

[Brian Haas]

Hi,

Could there be an incompatibility among versions of software/resources
being used? The compatibility matrix is here:
https://github.com/STAR-Fusion/STAR-Fusion/wiki/STAR-Fusion-release-and-CTAT-Genome-Lib-Compatibility-Matrix

Best way to run it is through our Singularity image:
https://github.com/STAR-Fusion/STAR-Fusion/wiki#want-to-use-singularity

hope this helps,

~b

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