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

[Daniel Tiezzi]

I'm running star 2-pass alignment (STAR 2.6) and having this issue during the intermediate index generation:

Jan 16 13:52:03 ..... started STAR run

Jan 16 13:52:03 ... starting to generate Genome files

Jan 16 13:53:38 ... starting to sort Suffix Array. This may take a long time...

Jan 16 13:54:08 ... sorting Suffix Array chunks and saving them to disk...

Jan 16 14:26:20 ... loading chunks from disk, packing SA...

Jan 16 14:28:18 ... finished generating suffix array

Jan 16 14:28:18 ... generating Suffix Array index

Jan 16 14:33:30 ... completed Suffix Array index

Jan 16 14:33:38 ..... 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

Jan 16 15:04:21 ...... FATAL ERROR, exiting

This is the last 20 lines in the Log.out file:

Writing 1701545800 bytes into /home/dtiezzi/Documents/star_genome_d1_vd1_gtfv22/SA_25 ; empty space on disk = 2270782787584 bytes ... done

Writing 1601298600 bytes into /home/dtiezzi/Documents/star_genome_d1_vd1_gtfv22/SA_26 ; empty space on disk = 2269081141248 bytes ... done

Writing 1636375792 bytes into /home/dtiezzi/Documents/star_genome_d1_vd1_gtfv22/SA_27 ; empty space on disk = 2267479834624 bytes ... done

Jan 16 14:26:20 ... loading chunks from disk, packing SA...

Jan 16 14:28:18 ... finished generating suffix array

Jan 16 14:28:18 ... generating Suffix Array index

Jan 16 14:33:30 ... completed Suffix Array index

Loaded database junctions from file: ./starOut/firstPassSJ.out.tab, total number of junctions: 2300971 junctions

Jan 16 14:33:33   Loaded database junctions from the pGe.sjdbFileChrStartEnd file(s), 2300971 total junctions

Jan 16 14:33:38   Finished preparing junctions

Jan 16 14:33:38 ..... inserting junctions into the genome indices

Jan 16 14:44:43   Finished SA search: number of new junctions=2300971, old junctions=0

Jan 16 15:04:21   Finished sorting SA indicesL nInd=920304372

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 16 15:04:21 ...... FATAL ERROR, exiting

This is my code:

STAR --runMode genomeGenerate --genomeDir ~/Documents/star_genome_d1_vd1_gtfv22 --genomeFastaFiles /mnt/md0/humanGenome/TCGA/GRCh38.d1.vd1.fa --sjdbOverhang 100 --runThreadN 8 --limitSjdbInsertNsj 3000000 --sjdbFileChrStartEnd ./starOut/firstPassSJ.out.tab

I have looked at similar previous threads and was not able to fix the problem.

The reads are mostly 100b long (some are bit shorter ~96-98).

Please, any help?

Cheers

daniel

[Alexander Dobin]

Hi Daniel,

please send me the Log.out file of the failed run.

Cheers

Alex