Trinity.tmp.fasta

[Lada Jovović]

Hi guys, 

Before, I used older Trinity versions and now I switched to the latest Trinity-v2.15.1 so some things are new. 

Can someone please confirm that Trinity.tmp.fasta is the expected output for the assembly ?

 

This tmp extension confused me as I am used to getting Trinity.fasta as output. My assembly at first look seems okay, I have the expected number of transcripts... 

I usually run my Trinity on a scratch disk, then everything is copied to my home folder and removed from scratch. 

I am getting this in the standard output: 

All commands completed successfully. :-)

 ** Harvesting all assembled transcripts into a single multi-fasta file...

Tuesday, February 13, 2024: 01:41:25    CMD: find /beegfs-fast/scratch/pbs.9246.admin/trinity_out_dir/read_partitions/ -name '*inity.fasta'  | /opt/conda/envs/trinity/opt/trinity-2.15.1/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /beegfs-fast/scratch/pbs.9246.admin/trinity_out_dir/Trinity.tmp

* [Tue Feb 13 01:44:33 2024] Running CMD: /opt/conda/envs/trinity/opt/trinity-2.15.1/util/support_scripts/salmon_runner.pl Trinity.tmp.fasta /beegfs-fast/scratch/pbs.9246.admin/trinity_out_dir/both.fa 60

* [Tue Feb 13 01:47:32 2024] Running CMD: /opt/conda/envs/trinity/opt/trinity-2.15.1/util/support_scripts/filter_transcripts_require_min_cov.pl Trinity.tmp.fasta /beegfs-fast/scratch/pbs.9246.admin/trinity_out_dir/both.fa salmon_outdir/quant.sf 2 > /beegfs-fast/scratch/pbs.9246.admin/trinity_out_dir.Trinity.fasta

Tuesday, February 13, 2024: 01:47:48    CMD: /opt/conda/envs/trinity/opt/trinity-2.15.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /beegfs-fast/scratch/pbs.9246.admin/trinity_out_dir.Trinity.fasta > /beegfs-fast/scratch/pbs.9246.admin/trinity_out_dir.Trinity.fasta.gene_trans_map

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Finished.  Final Trinity assemblies are written to /beegfs-fast/scratch/pbs.9246.admin/trinity_out_dir.Trinity.fasta

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Tnx!

Lada