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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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DBD::SQLite::st execute failed: database is locked #918

Open jimie0311 opened 1 year ago

jimie0311 commented 1 year ago

Are you using the latest release? Hello Sir, I am using funannotate 1.8.7 with the below command, but get an error of "the database is locked". Some issues suggested setting --CPU=1 or -T 1. Where should I set? The trinity part is finished, If I rerun, can I just start from pasa? Thanks

funannotate train -i hapB_cleaned.fasta -o fun --left /mnt/data/liyuanjie/Data/Sequencing_data/Puccinia_sorghi/timecourse/links/PSGS1_R1.fq.gz \ --right /mnt/data/liyuanjie/Data/Sequencing_data/Puccinia_sorghi/timecourse/links/PSGS1_R2.fq.gz\ --stranded no --jaccard_clip --species "ustilago maydis" --cpu 10

By running funannotate check --version You are running Python v 3.7.10. Now checking Python packages... biopython: 1.79 goatools: 1.1.6 matplotlib: 3.4.2 natsort: 7.1.1 numpy: 1.21.0 pandas: 1.3.0 psutil: 5.8.0 requests: 2.25.1 scikit-learn: 0.24.2 scipy: 1.7.0 seaborn: 0.11.1 All 11 python packages installed

You are running Perl v b'5.026002'. Now checking perl modules... Bio::Perl: 1.7.8 Carp: 1.38 Clone: 0.42 DBD::SQLite: 1.64 DBD::mysql: 4.046 DBI: 1.642 DB_File: 1.855 Data::Dumper: 2.173 File::Basename: 2.85 File::Which: 1.23 Getopt::Long: 2.5 Hash::Merge: 0.300 JSON: 4.02 LWP::UserAgent: 6.39 Logger::Simple: 2.0 POSIX: 1.76 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.12 Tie::File: 1.02 URI::Escape: 3.31 YAML: 1.29 threads: 2.15 threads::shared: 1.56 All 27 Perl modules installed

Checking Environmental Variables... $FUNANNOTATE_DB=/data/Liangjunmin/database/funannotate_db $PASAHOME=/data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1 $TRINITY_HOME=/data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/config/ $GENEMARK_PATH=/data/Liangjunmin/opt/biosoft/gm_et_linux_64/gmes_petap/ All 6 environmental variables are set

Checking external dependencies... PASA: 2.4.1 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.3.3 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v36 diamond: 2.0.8 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2017-11-15 gmes_petap.pl: 4.38 hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 11.0.8-internal kallisto: 0.46.1 mafft: v7.480 (2021/May/21) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.20-r1061 proteinortho: 6.0.31 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.10 signalp: 5.0b snap: 2006-07-28 stringtie: 2.1.7 tRNAscan-SE: 2.0.7 (Oct 2020) tantan: tantan 26 tbl2asn: no way to determine, likely 25.X tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 ERROR: emapper.py not installed

Logfiles The end of funannotate-train.log ..... Committed 177700
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done.

==== Failed query: <select al.align_id, al.align_acc from subcluster_link sl, align_link al where al.align_acc = sl.cdna_acc and sl.subcluster_id = ?> values: 3548 Errors: database is locked

Failed query: <select al.align_id, al.align_acc from subcluster_link sl, align_link al where al.align_acc = sl.cdna_acc and sl.subcluster_id = ?> values: 3548 Errors: at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/PerlLib/DB_connect.pm line 203. DB_connect::do_sql_2D(DB_connect=HASH(0x55818dc42918), "select al.align_id, al.align_acc from subcluster_link sl, ali"..., 3548) called at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/classify_alt_splice_isoforms_per_subcluster.dbi line 63 Thread 1084 terminated abnormally: Error, command /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/classify_alt_splice_isoforms_per_subcluster.dbi -M /mnt/data/liangjunmin/puccinia_sorghi/funannotate/hapB/fun/training/pasa/ustilago_maydis_pasa -s 3548 > tmp_classify_alt_isoforms/3548.out died with ret (2816). Maybe see tmp_classify_alt_isoforms/3548.out.temp for information at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/classify_alt_splice_isoforms.dbi line 284. ERROR, thread 1084 exited with error Error, command /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/classify_alt_splice_isoforms_per_subcluster.dbi -M /mnt/data/liangjunmin/puccinia_sorghi/funannotate/hapB/fun/training/pasa/ustilago_maydis_pasa -s 3548 > tmp_classify_alt_isoforms/3548.out died with ret (2816). Maybe see tmp_classify_alt_isoforms/3548.out.temp for information at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/classify_alt_splice_isoforms.dbi line 284.

Error, 1 threads failed. Error, cmd: /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/classify_alt_splice_isoforms.dbi -M '/mnt/data/liangjunmin/puccinia_sorghi/funannotate/hapB/fun/training/pasa/ustilago_maydis_pasa' -G /mnt/data/liangjunmin/puccinia_sorghi/funannotate/hapB/fun/training/genome.fasta -T 10 > pasa_run.log.dir/alt_splicing_analysis.out died with ret 7424 No such file or directory at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/PerlLib/Pipeliner.pm line 187. Pipeliner::run(Pipeliner=HASH(0x55b6d3c1bba8)) called at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/Launch_PASA_pipeline.pl line 1044

hyphaltip commented 1 year ago

pasa will restart from where it stopped last, if the DB is locked due to a failed process that left it in a locked state you may need to remove fun/training/pasa/ustilago_maydis_pasa and restart.

multithreading may not work well depending on your platform, running pasa with MySQL/MariaDB is much faster and supports multithreading more appropriately.

possibly see #916