[05/09/24 07:42:29]: /venv/lib/python3.8/site-packages/funannotate/aux_scripts/trinity.py -f fun/training/genome.fasta -o fun/training/trinity.fasta -b fun/training/hisat2.coordSorted.bam -t fun/training --stranded RF --max_intronlen 3000 --cpus 16 --TRINITYHOME /venv/opt/trinity-2.8.5 --memory 80G --logfile fun/logfiles/funannotate-trinity.log --jaccard_clip -l fun/training/normalize/left.norm.fq -r fun/training/normalize/right.norm.fq

[05/09/24 07:42:29]: Building Hisat2 genome index
[05/09/24 07:42:29]: hisat2-build -p 16 fun/training/genome.fasta fun/training/hisat2.genome
[05/09/24 07:46:30]: Aligning reads to genome using Hisat2
[05/09/24 07:46:30]: hisat2 -p 16 --max-intronlen 3000 --dta -x fun/training/hisat2.genome --rna-strandness RF -1 /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/normalize/left.norm.fq -2 /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/normalize/right.norm.fq | samtools sort --reference fun/training/genome.fasta -@ 8 -o fun/training/hisat2.coordSorted.bam -
[05/09/24 07:48:05]: Running genome-guided Trinity, logfile: fun/training/Trinity-gg.log
[05/09/24 07:48:05]: Clustering of reads from BAM and preparing assembly commands
[05/09/24 07:48:05]: Trinity --SS_lib_type RF --no_distributed_trinity_exec --genome_guided_bam fun/training/hisat2.coordSorted.bam --genome_guided_max_intron 3000 --CPU 16 --max_memory 80G --output fun/training/trinity_gg --jaccard_clip
[05/09/24 08:01:44]: Assembling 35,333 Trinity clusters using 15 CPUs
[05/09/24 11:37:32]: perl /venv/opt/trinity-2.8.5/util/support_scripts/GG_partitioned_trinity_aggregator.pl Trinity_GG
[05/09/24 11:37:32]: 60,037 transcripts derived from Trinity