EXITING because of FATAL PARAMETER ERROR

[ahsmith22]

I know this error has been resolved in other posts, but those solutions did not work for me. This is the output that I am getting:

mkdir: cannot create directory '7321.1.67340.GGTAGC.fastq': File exists STAR --runMode genomeGenerate --runThreadN 24 --genomeSAsparseD 3 --genomeSAindexNbases 12 --genomeChrBinNbits 14 --genomeDir 7321.1.67340.GGTAGC.fastq --genomeFastaFiles ./Raw_Data/7321.1.67340.GGTAGC.fasta --sjdbGTFfile Suilu4_GeneCatalog_20170628.gtf --sjdbOverhang 150 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 11 19:09:50 ..... started STAR run Jun 11 19:09:51 ... starting to generate Genome files

EXITING because of FATAL PARAMETER ERROR: limitGenomeGenerateRAM=31000000000is too small for your genome SOLUTION: please specify --limitGenomeGenerateRAM not less than 8927894219701 and make that much RAM available

Jun 11 19:25:40 ...... FATAL ERROR, exiting done

I have tried adding additional tags (genomeSAsparseD, genomeSAindexNbases, genomeChrBinNbits) to no avail. If there's anything else I can try that would be great. Thanks!

[YPHa]

Hi, Not sure if this is the case here, but I believe a directory can only have unique files within it. And directories are also considered files. So make sure that you pick a different file and directory name. Hope this helps,

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From: ahsmith22 @.> Sent: Monday, June 20, 2022 4:33 AM To: alexdobin/STAR @.> Cc: Subscribed @.***> Subject: [alexdobin/STAR] EXITING because of FATAL PARAMETER ERROR (Issue #1587)

I know this error has been resolved in other posts, but those solutions did not work for me. This is the output that I am getting:

mkdir: cannot create directory '7321.1.67340.GGTAGC.fastq': File exists STAR --runMode genomeGenerate --runThreadN 24 --genomeSAsparseD 3 --genomeSAindexNbases 12 --genomeChrBinNbits 14 --genomeDir 7321.1.67340.GGTAGC.fastq --genomeFastaFiles ./Raw_Data/7321.1.67340.GGTAGC.fasta --sjdbGTFfile Suilu4_GeneCatalog_20170628.gtf --sjdbOverhang 150 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 11 19:09:50 ..... started STAR run Jun 11 19:09:51 ... starting to generate Genome files

EXITING because of FATAL PARAMETER ERROR: limitGenomeGenerateRAM=31000000000is too small for your genome SOLUTION: please specify --limitGenomeGenerateRAM not less than 8927894219701 and make that much RAM available

Jun 11 19:25:40 ...... FATAL ERROR, exiting done

I have tried adding additional tags (genomeSAsparseD, genomeSAindexNbases, genomeChrBinNbits) to no avail. If there's anything else I can try that would be great. Thanks!

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[alexdobin]

Hi @ahsmith22

according to the error message, this genome would require ~8TB of RAM. What are the size of the genome and the number of "chromosomes"?

[ahsmith22]

Hi @alexdobin !

This genome is about 44 megabases, 16,000 genes, but I do not know how many chromosomes since this number is variable within this species.

Thanks!

[ahsmith22]

Hey @alexdobin,

I was able to run the index command with the desired amount of RAM and I am getting a new error:

Fatal INPUT FILE error, no valid exon lines in the GTF file: Suilu4_GeneCatalog_20170628.gtf Solution: check the formatting of the GTF file. One likely cause is the difference in chromosome naming between GTF and FASTA file.

I am obtaining both genome and annotation files from here: https://mycocosm.jgi.doe.gov/Suilu4/Suilu4.home.html

The annotation file comes as a gff file and so I am using agat to convert to gff. The genome files comes as a fastq file so I converted to fasta.

Any help is much appreciated! Alex

[alexdobin]

Hi Alex,

you need to make sure that the chromosome names in the GTF and FASTA files coincide.

Cheers Alex