brianjohnhaas
commented
1 year ago Hi Emily,
When it crashes at the STAR step it's usually because of insufficient RAM. Can you make sure it's on a machine where you can allocate ~50G of RAM to it?
best,
~b
On Fri, Sep 29, 2023 at 10:39 AM Emily Hoskins @.***> wrote:
Hi!
I'm trying to run STAR-Fusion with the coding effect option. Here is the command that I ran:
`cd /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/sartor_2022/SRR2932813/
/fs/ess/PAS0854/Software/STAR-Fusion/STAR-Fusion-v1.6.0/STAR-Fusion --left_fq /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/sartor_2022/SRR2932813/SRR2932813_1.fastq.gz --right_fq /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/sartor_2022/SRR2932813/SRR2932813_2.fastq.gz --genome_lib_dir /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/rna_analysis/GRCh38_gencode_v29_CTAT_lib_Mar272019.plug-n-play/ctat_genome_lib_build_dir/ --examine_coding_effect`
Here is the output I got:
`CMD: mkdir -p /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/sartor_2022/SRR2932813/STAR-Fusion_outdir CMD: mkdir -p /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/sartor_2022/SRR2932813/STAR-Fusion_outdir/_starF_checkpoints CMD: mkdir -p /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/sartor_2022/SRR2932813/STAR-Fusion_outdir/star-fusion.preliminary
- Running CMD: /fs/project/PAS0854/Software/STAR_Latest/STAR-2.7.0f/bin/Linux_x86_64/STAR --genomeDir /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/rna_analysis/GRCh38_gencode_v29_CTAT_lib_Mar272019.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 /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/sartor_2022/SRR2932813/SRR2932813_1.fastq.gz /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/sartor_2022/SRR2932813/SRR2932813_2.fastq.gz --outSAMattrRGline ID:GRPundef --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --genomeLoad NoSharedMemory --twopassMode Basic --readFilesCommand 'gunzip -c' Sep 28 17:58:20 ..... started STAR run Sep 28 17:58:20 ..... loading genome Sep 28 17:58:44 ..... started 1st pass mapping Sep 28 18:25:42 ..... finished 1st pass mapping Sep 28 18:25:43 ..... inserting junctions into the genome indices Error, cmd: /fs/project/PAS0854/Software/STAR_Latest/STAR-2.7.0f/bin/Linux_x86_64/STAR --genomeDir /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/rna_analysis/GRCh38_gencode_v29_CTAT_lib_Mar272019.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 /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/sartor_2022/SRR2932813/SRR2932813_1.fastq.gz /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/sartor_2022/SRR2932813/SRR2932813_2.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 135 No such file or directory at /fs/ess/PAS0854/Software/STAR-Fusion/STAR-Fusion-v1.6.0/PerlLib/Pipeliner.pm line 181. Pipeliner::run('Pipeliner=HASH(0x2287468)') called at /fs/ess/PAS0854/Software/STAR-Fusion/STAR-Fusion-v1.6.0/STAR-Fusion line 866 main::run_STAR('Pipeliner=HASH(0x2287468)', '/fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets...', '/fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets...', '') called at /fs/ess/PAS0854/Software/STAR-Fusion/STAR-Fusion-v1.6.0/STAR-Fusion line 511`
I checked to make sure that the fastq.gz files are in the working directory. Also, /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/rna_analysis/GRCh38_gencode_v29_CTAT_lib_Mar272019.plug-n-play/ctat_genome_lib_build_dir/ is an existing directory. Is there something else that I may be missing?
I appreciate your help!
Emily
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
nadia35
PikalaxALT
Hi!
I'm trying to run STAR-Fusion with the coding effect option. Here is the command that I ran:
Here is the output I got:
I checked to make sure that the fastq.gz files are in the working directory. Also, /fs/ess/PAS0854/Emily/kinase_fusions/head_neck/other_datasets/rna_analysis/GRCh38_gencode_v29_CTAT_lib_Mar272019.plug-n-play/ctat_genome_lib_build_dir/ is an existing directory. Is there something else that I may be missing?
I appreciate your help!
Emily