Hanging at Loading genome

[akiselev-lrsv]

Hello! First, thank you for the great job!

I have a problem with STAR running on cluster. The algortihm hangs forever at the 'loading genome' stage. The last string in log.out file is 'inserting extra sequence to genome'

I ran STAR wit following options

STAR --genomeFastaFiles ~/work/reference/MtrunA17/MtrunA17r5.0-20161119-ANR.fasta --genomeDir ~/work/reference/MtrunA17 \ --sjdbGTFfile ~/work/reference/MtrunA17/MtrunA17r5.0-ANR-EGN-r1.6.gtf \ --outSAMtype BAM SortedByCoordinate \ --outSAMstrandField intrnoMotif --alignSoftClipAtReferenceEnds No \ --outFilterIntronMotifs RemoveNoncanonical --quantMode TranscriptomeSAM GeneCounts \ --sjdbFileChrStartEnd ~/work/reference/MtrunA17/ChrStartEnd.tab \ --readFilesIn 28_uniq_properpaired_R1_val_1.fq 28_uniq_properpaired_R2_val_2.fq \ --outFileNamePrefix ~/work/RNAseq_Medicago_Aphano/STAR/28

Do you have any suggestions to overcome this?

Thank you!

[alexdobin]

Hi @akiselev-lrsv

In the genome generation step you need to use: STAR --genomeFastaFiles ~/work/reference/MtrunA17/MtrunA17r5.0-20161119-ANR.fasta --genomeDir ~/work/reference/MtrunA17 --sjdbGTFfile ~/work/reference/MtrunA17/MtrunA17r5.0-ANR-EGN-r1.6.gtf Then, at the mapping step, do not use --genomeFastaFiles and --sjdbGTFfile again.

--sjdbFileChrStartEnd ~/work/reference/MtrunA17/ChrStartEnd.tab where did this file come from? If it's from the same GTF as before, you do not need to use. `

--outSAMstrandField intrnoMotif ` is spelled wrong, should intronMotif

Also, for both genome generation and mapping, you can use multiple threads (at least = number of cores), e.g. --runThreadN 12

Cheers Alex