"cannot insert junctions on the fly because of strand GstrandBit problem

DE

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Sep 13, 2016, 11:40:47 AM9/13/16

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Hi Alex,

I am trying to build the rheMac8 genome with a .gtf annotation file using STAR 2.5.2a and keep running into the following error:

========================================

Sep 12 15:09:58 ..... started STAR run

Sep 12 15:09:58 ... starting to generate Genome files

Sep 12 15:11:30 ... starting to sort Suffix Array. This may take a long time...

Sep 12 15:11:54 ... sorting Suffix Array chunks and saving them to disk...

Sep 12 15:51:40 ... loading chunks from disk, packing SA...

Sep 12 16:06:28 ... finished generating suffix array

Sep 12 16:06:28 ... generating Suffix Array index

Sep 12 16:06:39 ... completed Suffix Array index

Sep 12 16:06:39 ..... processing annotations GTF

Sep 12 16:06:40 ..... 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

Sep 12 16:06:59 ...... FATAL ERROR, exiting

========================================

Below is the code I am running:

STAR --runThreadN $SLURM_CPUS_PER_TASK --runMode genomeGenerate --genomeDir $BUILDLOCATION --genomeFastaFiles rheMac8.fa --sjdbGTFfile my_annotation.gtf --sjdbOverhang 99 --genomeSAindexNbases 11 --genomeChrBinNbits 12

I have the Log.out file, how can I send it to you?

Thanks!

DE

Alexander Dobin

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Sep 14, 2016, 12:32:20 PM9/14/16

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Hi DE

2.5.2a was supposed to fix the problem... Please zip the Log.out file and send it to dobin @ cshl edu

Cheers

Alex

Feifei

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Nov 7, 2016, 2:22:43 PM11/7/16

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Any updates on this? I'm getting the same error on the newest STAR v2.5.2b. I can also send you the Log file.

Alexander Dobin

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Nov 8, 2016, 6:42:12 PM11/8/16

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Hi Feifei,

Please send me the Log.out file.

Cheers

Alex

Monika Michalovová

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Dec 5, 2016, 4:05:28 PM12/5/16

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Same problem here. Please see attached.
Thank you,

Monika

On Tuesday, September 13, 2016 at 11:40:47 AM UTC-4, DE wrote:

Log.out

Alexander Dobin

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Dec 5, 2016, 4:36:29 PM12/5/16

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Hi Monika,

--genomeFastaFiles is typically only used at the genome generation step. You can use at the mapping step only if you want to add extra reference sequences that were not present at the genome generation step. it looks like you are using the same file in both steps, which causes the problem. If you omit this parameter from the mapping run, it should work fine.