Error message during genomeGenerate

[Sandy Jan Labarosa]

I am trying to make a genome index for mapping and I keep getting this error:

EXITING because of FATAL ERROR: cannot insert junctions on the fly because of strand GstrandBit problem
SOLUTION: please contact STAR author at https://groups.google.com/forum/#!forum/rna-star

Dec 22 14:13:43 ...... FATAL ERROR, exiting

I already followed the instructions given here: 

https://groups.google.com/g/rna-star/c/LOj0z9oWoNU

https://github.com/alexdobin/STAR/issues/1392

https://github.com/alexdobin/STAR/issues/1194

However, the error still persists.

Here is the script I used:

STAR --runThreadN 11 \
--limitBAMsortRAM 75000000000 \
--runMode genomeGenerate \
--genomeDir "$Output/$Species" \
--genomeFastaFiles "$Reference_genome" \
--sjdbGTFfile "$Annotation_file" \
--sjdbGTFtagExonParentTranscript Parent \
--limitSjdbInsertNsj 4000000 \
--sjdbOverhang 149

The annotation file I used is a .gff3, below is the snippet of the annotation file.

Hsteno_chr1H    Liftoff    gene    26124    32988    .    -    .    ID=Hsteno-30543
Hsteno_chr1H    Liftoff    mRNA    26124    32988    .    -    .    ID=Hsteno-30543.1;Parent=Hsteno-30543;Dbxref=InterPro:IPR039199,InterPro:IPR028097,InterPro:IPR028091,MobiDBLite:mobidb-lite,PANTHER:PTHR28441,Pfam:PF14648,Pfam:PF14647
Hsteno_chr1H    Liftoff    exon    26124    26596    .    -    .    ID=Hsteno-30543.1-exon1;Parent=Hsteno-30543.1
Hsteno_chr1H    Liftoff    exon    26717    28301    .    -    .    ID=Hsteno-30543.1-exon2;Parent=Hsteno-30543.1
Hsteno_chr1H    Liftoff    exon    28510    28874    .    -    .    ID=Hsteno-30543.1-exon3;Parent=Hsteno-30543.1
Hsteno_chr1H    Liftoff    exon    29021    29081    .    -    .    ID=Hsteno-30543.1-exon4;Parent=Hsteno-30543.1
Hsteno_chr1H    Liftoff    exon    29280    29433    .    -    .    ID=Hsteno-30543.1-exon5;Parent=Hsteno-30543.1

Any help would be appreciated. Thank you very much. 

Best,

Sandy

[Alexander Dobin]

Hi Sandy,

please send me the Log.out file.

Cheers

Alex

[Sandy Jan Labarosa]

Dear Alex,

I apologize for the late reply.

Unfortunately, I cannot attach the log file directly here due to large size (>80 mb) but you can download it from this link:

https://uni-duesseldorf.sciebo.de/s/lbyvpJ7191OUdOH

Thank you very much for your support.

Best,

Sandy

[Alexander Dobin]

Hi Sandy,

You are using a very old version of STAR. Please switch to the latest one, and this will likely go away:

https://github.com/alexdobin/STAR/releases/tag/2.7.11a