![]() * Running CMD: /home/michaelk/anaconda3/envs/test/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes -genome_lib_dir /home/michaelk/downloads/star-fusion-v1.3/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -J > /scratch/10521398/tmp.cL8ZoGpsnC/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt My error message is very similar, but the On Tue, at 2:25 PM, Michael Knudsen wrote: Pipeliner::run(Pipeliner=HASH(0x17771b0)) called at /home/michaelk/anaconda3/envs/starfusion/lib/STAR-Fusion/STAR-Fusion line 659 Intervals must have positive width at /home/michaelk/anaconda3/envs/starfusion/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes line 570, line 116978.Įrror, cmd: /home/michaelk/anaconda3/envs/starfusion/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes -genome_lib_dir /faststorage/project/MomaRAWfiles/BACKUP/reference/star/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -J > /faststorage/home/michaelk/NOT_BACKUP/fusion/pipeline/star_fusion/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt died with ret 6400 No such file or directory at /home/michaelk/anaconda3/envs/starfusion/lib/STAR-Fusion/PerlLib/Pipeliner.pm line 178. building interval tree based on /faststorage/project/MomaRAWfiles/BACKUP/reference/star/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_ * Running CMD: /home/michaelk/anaconda3/envs/starfusion/lib/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes -genome_lib_dir /faststorage/project/MomaRAWfiles/BACKUP/reference/star/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -J > /faststorage/home/michaelk/NOT_BACKUP/fusion/pipeline/star_fusion/star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt inserting junctions into the genome indicesĪpr 17 20:13:14. finished 1st pass mappingĪpr 17 20:05:52. * Running CMD: /home/michaelk/anaconda3/envs/starfusion/bin/STAR -genomeDir /faststorage/project/MomaRAWfiles/BACKUP/reference/star/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx -readFilesIn /faststorage/home/michaelk/NOT_BACKUP/fusion/pipeline/merged_R1.fastq.gz /faststorage/home/michaelk/NOT_BACKUP/fusion/pipeline/merged_R2.fastq.gz -outReadsUnmapped None -chimSegmentMin 12 -chimJunctionOverhangMin 12 -alignSJDBoverhangMin 10 -alignMatesGapMax 100000 -alignIntronMax 100000 -alignSJstitchMismatchNmax 5 -1 5 5 -runThreadN 36 -outSAMstrandField intronMotif -outSAMunmapped Within -outSAMtype BAM Unsorted -outSAMattrRGline ID:GRPundef -chimSegmentReadGapMax 3 -genomeLoad NoSharedMemory -twopassMode Basic -readFilesCommand 'gunzip -c'Īpr 17 20:03:18. Reply to this email directly, view it on GitHubĬMD: mkdir -p /faststorage/home/michaelk/NOT_BACKUP/fusion/pipeline/star_fusion/_starF_checkpointsĬMD: mkdir -p /faststorage/home/michaelk/NOT_BACKUP/fusion/pipeline/star_fusion/star-fusion.preliminary You are receiving this because you commented. softwares/STAR-Fusion-v1.3.2/STAR-Fusion line 659 Pipeliner::run('Pipeliner=HASH(0x1200a10)') called at softwares/STAR-Fusion-v1.3.2/PerlLib/Pipeliner.pm line 178 c' *died with ret 9 No such file or directory* at genomeLoad NoSharedMemory -twopassMode Basic -readFilesCommand 'gunzip ![]() Unsorted -outSAMattrRGline ID:GRPundef -chimSegmentReadGapMax 3 outSAMstrandField intronMotif -outSAMunmapped Within -outSAMtype BAM alignSJDBoverhangMin 10 -alignMatesGapMax 100000 -alignIntronMaxġ00000 -alignSJstitchMismatchNmax 5 -1 5 5 -runThreadN 4 readFilesIn fastqdir/S01_S1_R1_įastqdir/S01_S1_R2_ -outReadsUnmapped None -chimSegmentMin It seemed to have run okay for a little bit before giving the error, this Let me know if you need any other information. Pipeliner::run('Pipeliner=HASH(0x1200a10)') called at /softwares/STAR-Fusion-v1.3.2/STAR-Fusion line 659 genomeLoad NoSharedMemory -twopassMode Basic -readFilesCommand 'gunzip -c' died with ret 9 No such file or directory at /softwares/STAR-Fusion-v1.3.2/PerlLib/Pipeliner.pm line 178 ![]() outSAMstrandField intronMotif -outSAMunmapped Within -outSAMtype BAM Unsorted -outSAMattrRGline ID:GRPundef -chimSegmentReadGapMax 3 alignSJDBoverhangMin 10 -alignMatesGapMax 100000 -alignIntronMax 100000 -alignSJstitchMismatchNmax 5 -1 5 5 -runThreadN 4 readFilesIn fastqdir/S01_S1_R1_ fastqdir/S01_S1_R2_ -outReadsUnmapped None -chimSegmentMin 12 -chimJunctionOverhangMin 12 It seemed to have run okay for a little bit before giving the error, this was the exact output:Įrror, cmd: /softwares/STAR-2.5.3a/bin/Linux_x86_64/STAR -genomeDir /genomes/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx genome_lib_dir /genomes/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir ![]() softwares/STAR-Fusion-v1.3.2/STAR-Fusion
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