FATAL ERROR: cannot insert junctions on the fly because of strand GstrandBit problem

[christian...@gmail.com]

Hi Alex,
     I was building an index with --runMode genomeGenerate when received the error in the subject line of this email. I am using STAR_2.5.1b. Here is the complete output of my process:

Linux_x86_64_static/STAR --runThreadN 7 --runMode genomeGenerate --genomeDir ./ --genomeFastaFiles ../hg38.fa --sjdbOverhang 149 \
--sjdbFileChrStartEnd ../intropolis.v1.hg38_filt.tsv --sjdbGTFfile CGDB.gtf  --limitSjdbInsertNsj 20000000 --limitGenomeGenerateRAM 150000000000

May 05 13:52:25 ..... Started STAR run
May 05 13:52:25 ... Starting to generate Genome files
May 05 13:53:38 ... starting to sort  Suffix Array. This may take a long time...
May 05 13:53:54 ... sorting Suffix Array chunks and saving them to disk...
May 05 14:40:42 ... loading chunks from disk, packing SA...
May 05 14:41:50 ... Finished generating suffix array
May 05 14:41:50 ... Generating Suffix Array index
May 05 14:45:12 ... Completed Suffix Array index
May 05 14:45:29 ..... Processing annotations GTF
May 05 14:46:20 ..... Inserting junctions into the genome indices

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

May 05 15:27:00 ...... FATAL ERROR, exiting

[Alexander Dobin]

Hi Chirstian,

this problem is caused by the large number of junctions you are adding to the genome.

2M junctions with 149 overhang add ~1Gbase of sequence to the genome, which crosses the 4GB boundary.

I will make a patch to resolve this issues, for now please reduce --sjdbOverhang, usually you do not need more than 100b.

Cheers

Alex

[Alexander Dobin]

Hi Christian,

please try the latest release https://github.com/alexdobin/STAR/releases/tag/2.5.2a,

I have fixed the GstrandBit problem.

Cheers

Alex

[Amir Foroushani]

Hi Alex,

I get a similar error with 2.5.2a . I have tried both STAR and STARlong. 

The reads are 454/Roche (from this paper http://www.g3journal.org/content/3/3/387.long). 

Average length is around 600, so I set the --sjdbOverhang 599

nohup STARlong --genomeDir /data/GenomeDir38Hs599 --runMode genomeGenerate --genomeFastaFiles /data/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /data/Homo_sapiens.GRCh38.85.gtf --sjdbOverhang 599 --runThreadN 32

This runs for a while and then:

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

Jan 13 18:14:27 ...... FATAL ERROR, exiting

What would you suggest?

Thanks,

Amir

[Alexander Dobin]

Hi Amir,

please use --sjdbOverhang 100 for the long reads of variable length. Going above this value does not improve alignments.

Cheers

Alex