pasa binary [] isn't executable or couldn't be found

[Anjali]

Hi,

I have done the alignment assembly step.

/scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/Launch_PASA_pipeline.pl -c alignAssemblyp.config -C -R -g hybrid_1.fasta -t transcripts_renamed.fasta.clean -T -u transcripts_renamed.fasta -f FL_accs.txt --ALIGNERS blat

But it gives an error:

Thread 381 terminated abnormally: Error, pasa binary [] isn't executable or couldn't be found. at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 66 thread 381, <$fh> line 91.         CDNA::PASA_alignment_assembler::_init(CDNA::PASA_alignment_assembler=HASH(0x5623332abdf8)) called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 52 thread 381              CDNA::PASA_alignment_assembler::new("CDNA::PASA_alignment_assembler") called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/scripts/assemble_clusters.dbi line 179 thread 381                                             main::assemble_transcripts_on_scaffold("SCAFFOLD2378_pilon") called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/scripts/assemble_clusters.dbi line 135 thread 381                                                      eval {...} called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/scripts/assemble_clusters.dbi line 135 thread 381                                                                                                ERROR, thread 381 exited with error Error, pasa binary [] isn't executable or couldn't be found. at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 66 thread 381, <$fh> line 91.                                                                                                                                                                                                                                                    CDNA::PASA_alignment_assembler::_init(CDNA::PASA_alignment_assembler=HASH(0x5623332abdf8)) called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 52 thread 381              CDNA::PASA_alignment_assembler::new("CDNA::PASA_alignment_assembler") called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/scripts/assemble_clusters.dbi line 179 thread 381                                             main::assemble_transcripts_on_scaffold("SCAFFOLD2378_pilon") called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/scripts/assemble_clusters.dbi line 135 thread 381                                                      eval {...} called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/scripts/assemble_clusters.dbi line 135 thread 381                                                                                                                                                                                                                                                                                                                                             Thread 817 terminated abnormally: Error, pasa binary [] isn't executable or couldn't be found. at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 66 thread 817.                        CDNA::PASA_alignment_assembler::_init(CDNA::PASA_alignment_assembler=HASH(0x562333dae4e8)) called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 52 thread 817              CDNA::PASA_alignment_assembler::new("CDNA::PASA_alignment_assembler") called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/scripts/assemble_clusters.dbi line 179 thread 817                                             main::assemble_transcripts_on_scaffold("SCAFFOLD470_pilon") called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/scripts/assemble_clusters.dbi line 135 thread 817                                                       eval {...} called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/scripts/assemble_clusters.dbi line 135 thread 817                                                                                                ERROR, thread 817 exited with error Error, pasa binary [] isn't executable or couldn't be found. at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 66 thread 817.                      CDNA::PASA_alignment_assembler::_init(CDNA::PASA_alignment_assembler=HASH(0x562333dae4e8)) called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 52 thread 817              CDNA::PASA_alignment_assembler::new("CDNA::PASA_alignment_assembler") called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/scripts/assemble_clusters.dbi line 179 thread 817                                             main::assemble_transcripts_on_scaffold("SCAFFOLD470_pilon") called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/scripts/assemble_clusters.dbi line 135 thread 817                                                       eval {...} called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/scripts/assemble_clusters.dbi line 135 thread 817                                                                                                                                                                                                                                                                                                                                             Error, 2 threads failed.                                                                                                                                                                                                                     Error, cmd: /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/scripts/assemble_clusters.dbi -G ../hybrid_1.fasta  -M '/scratch/anjalir/pasa/new/pasapp_db.sqlite'  -T 2  > pasapp_db.sqlite.pasa_alignment_assembly_building.ascii_illustrations.out died with ret 7424 No such file or directory at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/PerlLib/Pipeliner.pm line 187.                                                                                   Pipeliner::run(Pipeliner=HASH(0x55d65f650f98)) called at /scratch/anjalir/.miniconda3/envs/pasa_gmap_env/opt/pasa-2.4.1/Launch_PASA_pipeline.pl line 1044  

After that, I loaded the annotations and ran the annotations compare command, but again, no UTRs were added to my original annotations.

Load_Current_Gene_Annotations.dbi -c alignAssemblyp.config -g hybrid_1.fasta -P brakernew.gff3

Launch_PASA_pipeline.pl -c annotationComparep.config -A -g hybrid_1.fasta -t transcripts_renamed.fasta --ALT_SPLICE --TRANSDECODER

[Brian Haas]

Hi,

Did you run 'make' in the base pasapipeline software directory to build the pasa binary? This should compile it and put it in the software's PATH setting.

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Brian J. Haas
The Broad Institute
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[Anjali .]

Hi,

I installed PASA through conda.

[Brian Haas]

I see. I don't build the conda packages - not sure who does exactly - but it could be an issue with that.

Try just downloading the latest release and run 'make' in the base directory.  If that doesn't work, we have docker and singularity images - hopefully something will.