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Hi all
I started using STARFusion 1.6.0 with STAR 2.7.0f and got the error below
STAR-Fusion --genome_lib_dir /media/linuxfl/data/hg19STARFUSION --left_fq UPNT924_R1_Trimmed.fastq.gz --right_fq UPNT924_R3_Trimmed.fastq.gz --output_dir UNNT924_starfusion --FusionInspector inspect
* Running CMD: /home/linuxfl/STAR-2.7.0f/bin/Linux_x86_64//STAR --genomeDir /media/linuxfl/data/hg19STARFUSION/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 /media/linuxfl/data/CLIENT/RNA/UPNT924_R1_Trimmed.fastq.gz /media/linuxfl/data/CLIENT/RNA/UPNT924_R3_Trimmed.fastq.gz --outSAMattrRGline ID:GRPundef --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --genomeLoad NoSharedMemory --twopassMode Basic --readFilesCommand 'gunzip -c'
May 13 10:22:46 ..... started STAR run
May 13 10:22:46 ..... loading genome
May 13 10:26:37 ..... started 1st pass mapping
May 13 10:41:06 ..... finished 1st pass mapping
May 13 10:41:07 ..... inserting junctions into the genome indices
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted (core dumped)
Error, cmd: /home/linuxfl/STAR-2.7.0f/bin/Linux_x86_64//STAR --genomeDir /media/linuxfl/data/hg19STARFUSION/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 /media/linuxfl/data/RNA/UPNT924_R1_Trimmed.fastq.gz /media/linuxfl/data/RNA/UPNT924_R3_Trimmed.fastq.gz --outSAMattrRGline ID:GRPundef --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --genomeLoad NoSharedMemory --twopassMode Basic --readFilesCommand 'gunzip -c' died with ret 34304 No such file or directory at /home/linuxfl/STAR-Fusion/PerlLib/Pipeliner.pm line 181.
Pipeliner::run(Pipeliner=HASH(0x55afed976d30)) called at /home/linuxfl/STAR-Fusion/STAR-Fusion line 866
main::run_STAR(Pipeliner=HASH(0x55afed976d30), "/media/linuxfl/data/UPNT924_R1_Trimmed.fastq.gz", "/media/linuxfl/data/UPNT924_R3_Trimmed.fastq.gz", "") called at /home/linuxfl/STAR-Fusion/STAR-Fusion line 511
I have a linux 32Gb RAM
I have downloaded the CTAT plug an play ctat_genome_lib_building/GRCh37_gencode_v19_CTAT_lib_Mar272019
I have just unzip the zip file downloaded from the recommended ftp
Could you please help me?
Thanks
I started using STARFusion 1.6.0 with STAR 2.7.0f and got the error below
STAR-Fusion --genome_lib_dir /media/linuxfl/data/hg19STARFUSION --left_fq UPNT924_R1_Trimmed.fastq.gz --right_fq UPNT924_R3_Trimmed.fastq.gz --output_dir UNNT924_starfusion --FusionInspector inspect
* Running CMD: /home/linuxfl/STAR-2.7.0f/bin/Linux_x86_64//STAR --genomeDir /media/linuxfl/data/hg19STARFUSION/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 /media/linuxfl/data/CLIENT/RNA/UPNT924_R1_Trimmed.fastq.gz /media/linuxfl/data/CLIENT/RNA/UPNT924_R3_Trimmed.fastq.gz --outSAMattrRGline ID:GRPundef --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --genomeLoad NoSharedMemory --twopassMode Basic --readFilesCommand 'gunzip -c'
May 13 10:22:46 ..... started STAR run
May 13 10:22:46 ..... loading genome
May 13 10:26:37 ..... started 1st pass mapping
May 13 10:41:06 ..... finished 1st pass mapping
May 13 10:41:07 ..... inserting junctions into the genome indices
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted (core dumped)
Error, cmd: /home/linuxfl/STAR-2.7.0f/bin/Linux_x86_64//STAR --genomeDir /media/linuxfl/data/hg19STARFUSION/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 /media/linuxfl/data/RNA/UPNT924_R1_Trimmed.fastq.gz /media/linuxfl/data/RNA/UPNT924_R3_Trimmed.fastq.gz --outSAMattrRGline ID:GRPundef --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --genomeLoad NoSharedMemory --twopassMode Basic --readFilesCommand 'gunzip -c' died with ret 34304 No such file or directory at /home/linuxfl/STAR-Fusion/PerlLib/Pipeliner.pm line 181.
Pipeliner::run(Pipeliner=HASH(0x55afed976d30)) called at /home/linuxfl/STAR-Fusion/STAR-Fusion line 866
main::run_STAR(Pipeliner=HASH(0x55afed976d30), "/media/linuxfl/data/UPNT924_R1_Trimmed.fastq.gz", "/media/linuxfl/data/UPNT924_R3_Trimmed.fastq.gz", "") called at /home/linuxfl/STAR-Fusion/STAR-Fusion line 511
I have a linux 32Gb RAM
I have downloaded the CTAT plug an play ctat_genome_lib_building/GRCh37_gencode_v19_CTAT_lib_Mar272019
I have just unzip the zip file downloaded from the recommended ftp
Could you please help me?
Thanks