Trinity-GG.fasta empty file

[meera...@g.ucla.edu]

Hello,

I have tried running Trinity multiple times now, but I'm always running into an empty output Trinity-GG.fasta file, and I was hoping you could help me out with it.

I downloaded the Trinity Docker image through Singularity on the cluster, and I am using a sorted .bam file for a genome-guided transcriptome assembly. This is the command I used:

module load singularity; singularity exec -e trinityrnaseq_latest.sif Trinity --genome_guided_bam $SCRATCH/reannot/merged_aligned_reads.bam --genome_guided_max_intron 50000 --jaccard_clip --output $SCRATCH/reannot/trinity_GG --max_memory 15G --CPU 4 --SS_lib_type RF

The log file is too big to attach, but it seems to be giving no obvious error messages for the inputs, so I'm not sure what the issue is.

Thanks so much!

Best,

Meera

[Nicolas Delhomme]

Hej Meera!

This was a known issue in v2.13.1 , it's fixed in v2.13.2 relased Sept. 4. 

If you remove the trinity_GG.cmds.completed file and restart trinity, it should complete. Worked for me.

Nico 

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[meera...@g.ucla.edu]

Hi Nico,

I just downloaded the updated version, re-ran the same command and the issue is solved now, thanks so much for your response!

Meera