Describe the bug
I used this command to proceed funannotate train step, and I encountered with some errors associated with PASA. I did not use RNA seq libraries because I already have transcriptome assembly (genome guided), so I skipped the Trinity step. I also have iso-seq data, but it seems someone has the similar issue as I did #326 , so I dropped iso-seq data, reran the new one , and still faced the same error. Here is the command I used:
During funannotate train step, it generates this error
tAging/aging/TrimMapping/trinity_out_dir/Trinity-GG.fasta
[Feb 04 05:23 PM]: Removing poly-A sequences from trinity transcripts using seqclean
[Feb 04 06:10 PM]: Converting transcript alignments to GFF3 format
[Feb 04 06:10 PM]: Converting Trinity transcript alignments to GFF3 format
[Feb 04 06:11 PM]: Running PASA alignment step using 288,613 transcripts
Traceback (most recent call last):
File "/venv/bin/funannotate", line 8, in
sys.exit(main())
File "/venv/lib/python3.8/site-packages/funannotate/funannotate.py", line 716, in main
mod.main(arguments)
File "/venv/lib/python3.8/site-packages/funannotate/train.py", line 1175, in main
runPASAtrain(genome,
File "/venv/lib/python3.8/site-packages/funannotate/train.py", line 444, in runPASAtrain
with open(os.path.join(folder, pasaDBname+'.pasa_assemblies_described.txt'), 'r') as description:
FileNotFoundError: [Errno 2] No such file or directory: '/home/data/FLAG/PhormiaMaggotAging/funannotate/funannotate_train/RNA1/training/pasa/masked_pasa.pasa_assemblies_described.txt'"
Describe the bug I used this command to proceed funannotate train step, and I encountered with some errors associated with PASA. I did not use RNA seq libraries because I already have transcriptome assembly (genome guided), so I skipped the Trinity step. I also have iso-seq data, but it seems someone has the similar issue as I did #326 , so I dropped iso-seq data, reran the new one , and still faced the same error. Here is the command I used:
singularity exec --env GENEMARK_PATH=/home/slin023/gmes_linux_64_4/ --env PASAHOME=/home/data/FLAG/PhormiaMaggotAging/funannotate/PASApipeline-devel /home/slurmsample/singularity/funannotate_1.8.13.sif funannotate train -i /home/slin023/funannotate/masked.fasta --trinity /home/data/FLAG/PhormiaMaggotAging/aging/TrimMapping/trinity_out_dir/Trinity-GG.fasta --no_trimmomatic --cpus 1 -o /home/data/FLAG/PhormiaMaggotAging/funannotate/funannotate_train/RNA1 --memory 500G --aligners minimap2What command did you issue? funannotate 1.8.13
Logfiles
During funannotate train step, it generates this error
tAging/aging/TrimMapping/trinity_out_dir/Trinity-GG.fasta [Feb 04 05:23 PM]: Removing poly-A sequences from trinity transcripts using seqclean [Feb 04 06:10 PM]: Converting transcript alignments to GFF3 format [Feb 04 06:10 PM]: Converting Trinity transcript alignments to GFF3 format [Feb 04 06:11 PM]: Running PASA alignment step using 288,613 transcripts Traceback (most recent call last): File "/venv/bin/funannotate", line 8, in
sys.exit(main())
File "/venv/lib/python3.8/site-packages/funannotate/funannotate.py", line 716, in main
mod.main(arguments)
File "/venv/lib/python3.8/site-packages/funannotate/train.py", line 1175, in main
runPASAtrain(genome,
File "/venv/lib/python3.8/site-packages/funannotate/train.py", line 444, in runPASAtrain
with open(os.path.join(folder, pasaDBname+'.pasa_assemblies_described.txt'), 'r') as description:
FileNotFoundError: [Errno 2] No such file or directory: '/home/data/FLAG/PhormiaMaggotAging/funannotate/funannotate_train/RNA1/training/pasa/masked_pasa.pasa_assemblies_described.txt'"
If there is any suggestion, please let me know.