nextgenusfs
pasa-assembly problem
Are you using the latest release? yes
Describe the bug I have been running several funannotate update jobs in parallel and I get an error in earlier steps. It is strange because sometimes the sudden error happens and sometimes does not happens and the jobs are finished without error. I wonder if this is related to the jobs running in parallel.
Error: [May 19 04:03 PM]: CMD ERROR: /camp/home/safiand/home/users/safiand/.conda/envs/funannotate/opt/pasa-2.5.2/Launch_PASA_pipeline.pl -c /nemo/lab/cardoso-moreiam/home/users/safiand/genome_annotation/prolifica/funannotate/update/update_misc/pasa/alignAssembly.txt -r -C -R -g /nemo/lab/cardoso-moreiam/home/users/safiand/genome_annotation/prolifica/funannotate/update/update_misc/genome.fa --IMPORT_CUSTOM_ALIGNMENTS /nemo/lab/cardoso-moreiam/home/users/safiand/genome_annotation/prolifica/funannotate/update/update_misc/trinity.alignments.gff3 -T -t /nemo/lab/cardoso-moreiam/home/users/safiand/genome_annotation/prolifica/funannotate/update/update_misc/trinity.fasta.clean -u /nemo/lab/cardoso-moreiam/home/users/safiand/genome_annotation/prolifica/funannotate/update/update_misc/trinity.fasta --stringent_alignment_overlap 30.0 --TRANSDECODER --MAX_INTRON_LENGTH 3000 --CPU 20 --ALIGNERS blat
What command did you issue? funannotate update
Logfiles Please provide relavent log files of the error.
SQLite is single threaded, so if you are trying to access the same SQLite database in parallel that would probably be unsafe and cause errors?
It appears I had a memory problem as the jobs have been running ok since the memory was increased.