funannotate Restart after crash of the PASA training terminates normally

Hello I am trying to run the PASA training step (v. 1.8.11) with the following command but I get the following error

funannotate train -i $genome --cpus 1 -o $outdir -l $left -r $right --trinity $trinity_assembly

[Sep 15 10:33 AM]: OS: Ubuntu 18.10, 48 cores, ~ 264 GB RAM. Python: 3.6.8 [Sep 15 10:33 AM]: Running 1.8.11 [Sep 15 10:33 AM]: Trimmomatic will be skipped [Sep 15 10:33 AM]: Read normalization will be skipped [Sep 15 10:33 AM]: Parsing assembled trinity data : /mnt/sda1/Alex/09.GENOME_ANNOTATION/H_sp/03.TRANSCRIPTOME_ASSEMBLY/trinity_out_dir.Trinity.fasta [Sep 15 10:33 AM]: Removing poly-A sequences from trinity transcripts using seqclean [Sep 15 10:41 AM]: Converting transcript alignments to GFF3 format [Sep 15 10:41 AM]: Converting Trinity transcript alignments to GFF3 format [Sep 15 10:42 AM]: Running PASA alignment step using 183,389 transcripts [Sep 15 11:12 PM]: CMD ERROR: /mnt/sda1/Alex/software/PASApipeline-v2.5.2/Launch_PASA_pipeline.pl -c /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/H_sp/04.PASA_TRAINING/training/pasa/alignAssembly.txt -r -C -R -g /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/H_sp/04.PASA_TRAINING/training/genome.fasta --IMPORT_CUSTOM_ALIGNMENTS /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/H_sp/04.PASA_TRAINING/training/trinity.alignments.gff3 -T -t /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/H_sp/04.PASA_TRAINING/training/trinity.fasta.clean -u /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/H_sp/04.PASA_TRAINING/training/trinity.fasta --stringent_alignment_overlap 30.0 --TRANSDECODER --ALT_SPLICE --MAX_INTRON_LENGTH 3000 --CPU 1 --ALIGNERS blat

But when I restart it with the same command it seems to get past the point of the previous crash in the PASA pipeline. Are the results reliable in this case?

[Sep 16 03:47 PM]: OS: Ubuntu 18.10, 48 cores, ~ 264 GB RAM. Python: 3.6.8 [Sep 16 03:47 PM]: Running 1.8.11 [Sep 16 03:47 PM]: Trimmomatic will be skipped [Sep 16 03:47 PM]: Read normalization will be skipped [Sep 16 03:47 PM]: 183,396 existing Trinity results found: /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/H_sp/04.PASA_TRAINING/training/trinity.fasta [Sep 16 03:47 PM]: Removing poly-A sequences from trinity transcripts using seqclean [Sep 16 03:47 PM]: Existing SeqClean output found: /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/H_sp/04.PASA_TRAINING/training/trinity.fasta.clean [Sep 16 03:47 PM]: Existing BAM alignments found: /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/H_sp/04.PASA_TRAINING/training/trinity.alignments.bam, /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/H_sp/04.PASA_TRAINING/training/transcript.alignments.bam [Sep 16 03:47 PM]: Existing PASA assemblies found: /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/H_sp/04.PASA_TRAINING/training/pasa/H_sp_chrom_pasa.assemblies.fasta [Sep 16 03:47 PM]: PASA assigned 71,199 transcripts to 59,979 loci (genes) [Sep 16 03:47 PM]: Getting PASA models for training with TransDecoder [Sep 16 03:58 PM]: PASA finished. PASAweb accessible via: localhost:port/cgi-bin/index.cgi?db=/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/H_sp_chrom_pasa [Sep 16 03:58 PM]: Using Kallisto TPM data to determine which PASA gene models to select at each locus [Sep 16 03:58 PM]: Building Kallisto index [Sep 16 04:00 PM]: Mapping reads using pseudoalignment in Kallisto

Sep 16 '22 14:09 alexvasilikop

Look at the PASA logfile. If it started to write the output and then failed it might be incomplete. Funannotate isn't that smart to know if the file is truncated or complete.

Sep 16 '22 14:09 nextgenusfs

Where is this PASA log file located in the directory structure? Its name? thanks

Sep 16 '22 14:09 alexvasilikop

I'm the training folder, conspicuously named PASA.log

Sep 16 '22 14:09 nextgenusfs

Ok so here are the last lines of the /training/pasa/pasa-assembly.log:

[Thu Sep 15 11:32:25 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/extract_FL_transdecoder_entries.pl trinity.fasta.clean.transdecoder.gff3 > trinity.fasta.clean.transdecoder.gff3.fl_accs
[Thu Sep 15 11:32:26 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/update_fli_status.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -f trinity.fasta.clean.transdecoder.gff3.fl_accs
loading trinity.fasta.clean.transdecoder.gff3.fl_accs
[Thu Sep 15 12:43:35 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/validate_alignments_in_db.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -g /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/genome.fasta -t /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/trinity.fasta.clean --MAX_INTRON_LENGTH 3000 --CPU 1   --MIN_PERCENT_ALIGNED 90 --MIN_AVG_PER_ID 95 --NUM_BP_PERFECT_SPLICE_BOUNDARY 3 > alignment.validations.output
6 entries from file /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/genome.fasta were indexed in file /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/genome.fasta.cidx
183389 entries from file /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/trinity.fasta.clean were indexed in file /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/trinity.fasta.clean.cidx
-retrieving transcript sequences ... done.

Now validating alignments on scaffolds.
Processing 6/6      	(Chrom_6)                      
Done with alignment validations.
-capturing validation results from:
 /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/__tmp_alignment_validations/Chrom_6.alignment_validations.txt                                    * [Thu Sep 15 12:45:11 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/update_alignment_status.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' < alignment.validations.output  > pasa_run.log.dir/alignment.validation_loading.output
Committed 211832              
* [Thu Sep 15 12:45:42 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -v -A -P blat > Habrotrocha_sp_chrom_pasa.valid_blat_alignments.gff3
* [Thu Sep 15 12:45:54 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -v -A -P blat -B  > Habrotrocha_sp_chrom_pasa.valid_blat_alignments.bed
* [Thu Sep 15 12:46:10 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -v -A -P blat -T  > Habrotrocha_sp_chrom_pasa.valid_blat_alignments.gtf
* [Thu Sep 15 12:46:32 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -f -A -P blat > Habrotrocha_sp_chrom_pasa.failed_blat_alignments.gff3
-- Skipping CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -f -A -P blat -B  > Habrotrocha_sp_chrom_pasa.failed_blat_alignments.bed, checkpoint [/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/__pasa_Habrotrocha_sp_chrom_pasa_SQLite_chkpts/Habrotrocha_sp_chrom_pasa.failed_blat_alignments.gff3.ok] exists.
* [Thu Sep 15 12:46:41 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -f -A -P blat -T  > Habrotrocha_sp_chrom_pasa.failed_blat_alignments.gtf
* [Thu Sep 15 12:46:57 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -v -A -P custom > Habrotrocha_sp_chrom_pasa.valid_custom_alignments.gff3
* [Thu Sep 15 12:47:02 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -v -A -P custom -B  > Habrotrocha_sp_chrom_pasa.valid_custom_alignments.bed
* [Thu Sep 15 12:47:09 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -v -A -P custom -T  > Habrotrocha_sp_chrom_pasa.valid_custom_alignments.gtf
* [Thu Sep 15 12:47:20 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -f -A -P custom > Habrotrocha_sp_chrom_pasa.failed_custom_alignments.gff3
-- Skipping CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -f -A -P custom -B  > Habrotrocha_sp_chrom_pasa.failed_custom_alignments.bed, checkpoint [/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/__pasa_Habrotrocha_sp_chrom_pasa_SQLite_chkpts/Habrotrocha_sp_chrom_pasa.failed_custom_alignments.gff3.ok] exists.
* [Thu Sep 15 12:47:27 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -f -A -P custom -T  > Habrotrocha_sp_chrom_pasa.failed_custom_alignments.gtf
* [Thu Sep 15 12:47:40 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/polyA_site_transcript_mapper.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -c /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/trinity.fasta.cln -g /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/genome.fasta -t /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/trinity.fasta > pasa_run.log.dir/polyAsite_analysis.out
-missing faidx file: /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/trinity.fasta.fai, extracting positions directly.
-Fasta_retriever:: begin initializing for /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/trinity.fasta
-Fasta_retriever:: done initializing for /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/trinity.fasta
* [Thu Sep 15 12:49:22 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/polyA_site_summarizer.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -g /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/genome.fasta  > Habrotrocha_sp_chrom_pasa.polyAsites.fasta
* [Thu Sep 15 12:50:41 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/assign_clusters_by_stringent_alignment_overlap.dbi -M /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa -L 30.0 > pasa_run.log.dir/cluster_reassignment_by_stringent_overlap.out
// retrieving valid alignments.
// retrieving transcript coordinate data.
Will process 18 alignment assemblies...

Done!
* [Thu Sep 15 12:51:13 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/assemble_clusters.dbi -G /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/genome.fasta  -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa'  -T 1  > Habrotrocha_sp_chrom_pasa.pasa_alignment_assembly_building.ascii_illustrations.out
processes completed successfully.
* [Thu Sep 15 13:39:28 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/assembly_db_loader.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' > pasa_run.log.dir/alignment_assembly_loading.out
[6/6] scaffolds processed.            

Done.
* [Thu Sep 15 13:40:28 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/subcluster_builder.dbi -G /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/genome.fasta -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa'   -m 50 > pasa_run.log.dir/alignment_assembly_subclustering.out
Chrom_6* [Thu Sep 15 13:44:43 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/populate_mysql_assembly_alignment_field.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -G /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/genome.fasta
committed [71100] 
Done.
* [Thu Sep 15 13:45:45 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/populate_mysql_assembly_sequence_field.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -G /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/genome.fasta
* [Thu Sep 15 15:28:51 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/subcluster_loader.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa'  < pasa_run.log.dir/alignment_assembly_subclustering.out 
* [Thu Sep 15 18:56:02 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/alignment_assembly_to_gene_models.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -G /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/genome.fasta
Committed 284750  

done.
* [Thu Sep 15 19:06:57 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -a  > Habrotrocha_sp_chrom_pasa.pasa_assemblies.gff3
* [Thu Sep 15 19:07:07 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -a -B  > Habrotrocha_sp_chrom_pasa.pasa_assemblies.bed
* [Thu Sep 15 19:07:20 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/PASA_transcripts_and_assemblies_to_GFF3.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -a -T  > Habrotrocha_sp_chrom_pasa.pasa_assemblies.gtf
* [Thu Sep 15 19:07:38 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/describe_alignment_assemblies_cgi_convert.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa'  > Habrotrocha_sp_chrom_pasa.pasa_assemblies_described.txt
* [Thu Sep 15 19:07:53 2022] Running CMD: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/classify_alt_splice_isoforms.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -G /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/genome.fasta -T 1  > pasa_run.log.dir/alt_splicing_analysis.out
-in SQLite mode, disabling multithreading
DBD::SQLite::st execute failed: database is locked at /mnt/sda1/Alex/software/PASApipeline-v2.5.2//PerlLib/DB_connect.pm line 178.



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: 38933
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: 38933
Errors: 
 at /mnt/sda1/Alex/software/PASApipeline-v2.5.2//PerlLib/DB_connect.pm line 203.
	DB_connect::do_sql_2D(DB_connect=HASH(0x5627f6d48f78), "select al.align_id, al.align_acc from subcluster_link sl, ali"..., 38933) called at /mnt/sda1/Alex/software/PASApipeline-v2.5.2/scripts/classify_alt_splice_isoforms_per_subcluster.dbi line 63
Thread 3965 terminated abnormally: Error, command /mnt/sda1/Alex/software/PASApipeline-v2.5.2/scripts/classify_alt_splice_isoforms_per_subcluster.dbi -M /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa -s 38933 > __tmp_classify_alt_isoforms/38933.out died with ret (2816). Maybe see __tmp_classify_alt_isoforms/38933.out.temp for information at /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/classify_alt_splice_isoforms.dbi line 290.
ERROR, thread 3965 exited with error Error, command /mnt/sda1/Alex/software/PASApipeline-v2.5.2/scripts/classify_alt_splice_isoforms_per_subcluster.dbi -M /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa -s 38933 > __tmp_classify_alt_isoforms/38933.out died with ret (2816). Maybe see __tmp_classify_alt_isoforms/38933.out.temp for information at /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/classify_alt_splice_isoforms.dbi line 290.

Error, 1 threads failed.
Error, cmd: /mnt/sda1/Alex/software/PASApipeline-v2.5.2//scripts/classify_alt_splice_isoforms.dbi -M '/mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/pasa/Habrotrocha_sp_chrom_pasa' -G /mnt/sda1/Alex/09.GENOME_ANNOTATIONS/Habrotrocha_sp/04.PASA_TRAINING/training/genome.fasta -T 1  > pasa_run.log.dir/alt_splicing_analysis.out died with ret 6400 No such file or directory at /mnt/sda1/Alex/software/PASApipeline-v2.5.2//PerlLib/Pipeliner.pm line 187.
	Pipeliner::run(Pipeliner=HASH(0x56468cf71b08)) called at /mnt/sda1/Alex/software/PASApipeline-v2.5.2/Launch_PASA_pipeline.pl line 1047

Sep 16 '22 14:09 alexvasilikop

Sqlite database locked -- I can't remember why this happens, you can probably get some help at the PASA GitHub repo.

Sep 16 '22 16:09 nextgenusfs