Error: EXITING: Did not find the genome in memory, did not remove any genomes from shared memory

[lenshinaagbor]

Hi, I just came across this software as I have been struggling with MAKER. Running the example data and my data, I have encountered this same isssue. It says it can't find the genome but it's right there.

EXITING: Did not find the genome in memory, did not remove any genomes from shared memory This is what is on the log.out file;

cat Log.out STAR version=2.7.7a STAR compilation time,server,dir=Mon Dec 28 13:38:40 EST 2020 vega:/home/dobin/data/STAR/STARcode/STAR.master/source

Command Line: STAR --runThreadN 30 --genomeLoad Remove --genomeDir /mnt/nfs/home/b9017460/finder/example/star_index_without_transcriptome

Initial USER parameters from Command Line: All USER parameters from Command Line: runThreadN 30 ~RE-DEFINED genomeLoad Remove ~RE-DEFINED genomeDir /mnt/nfs/home/b9017460/finder/example/star_index_without_transcriptome ~RE-DEFINED

Finished reading parameters from all sources Final user re-defined parameters-----------------: runThreadN 30 genomeDir /mnt/nfs/home/b9017460/finder/example/star_index_without_transcriptome genomeLoad Remove

Final effective command line: STAR --runThreadN 30 --genomeDir /mnt/nfs/home/b9017460/finder/example/star_index_without_transcriptome --genomeLoad Remove Number of fastq files for each mate = 1 Finished loading and checking parameters Reading genome generation parameters:

STAR --runMode genomeGenerate --runThreadN 30 --genomeDir star_index_without_transcriptome --genomeFastaFiles Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa --genomeSAindexNbases 12 GstrandBit=32 versionGenome 2.7.4a ~RE-DEFINED genomeType Full ~RE-DEFINED genomeFastaFiles Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa ~RE-DEFINED genomeSAindexNbases 12 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED genomeTransformType None ~RE-DEFINED genomeTransformVCF - ~RE-DEFINED sjdbOverhang 0 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile - ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 120586240 985722733 ~RE-DEFINED Genome version is compatible with current STAR Number of real (reference) chromosomes= 7 1 1 30427671 0 2 2 19698289 30670848 3 3 23459830 50593792 4 4 18585056 74186752 5 5 26975502 92798976 6 Mt 366924 119799808 7 Pt 154478 120324096 Started loading the genome: Fri Jun 18 10:22:22 2021

Genome: size given as a parameter = 120586240 SA: size given as a parameter = 985722733 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=12 nSAi=22369620 nGenome=120586240; nSAbyte=985722733 GstrandBit=32 SA number of indices=238963086

EXITING: Did not find the genome in memory, did not remove any genomes from shared memory

Jun 18 10:22:22 ...... FATAL ERROR, exiting

Please help. I have tried adding the location but still not working :( I have been trying to annotate a genome for a very long time now but keep encountering errors.

Best, Lenshina