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

[jimie0311]

Are you using the latest release? If you are not using the latest release of funannotate, please upgrade, if bug persists then report here. I am using funannotate 1.8.7 Describe the bug The funannotate train and predict were run successfully and the error was came up when run update command. The error reported that pasa binary [] isn't executable or couldn't be found, however, I checked the pasa path in funannotate environment, it is executable. -rwxrwxr-x 3 user user 186152 Mar 25 2021 /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/bin/pasa

[10/08/21 12:26:48]: Running PASA annotation comparison step 1 [10/08/21 12:26:48]: /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/Launch_PASA_pipeline.pl -c /mnt/data/liangjunmin/asm4_canu2.1/hap1_2/emboss/hap1_2/funannotate2/hap2/fun_rna/update_misc/pasa/annotCompare.txt -g /mnt/data/liangjunmin/asm4_canu2.1/hap1_2/emboss/hap1_2/funannotate2/hap2/fun_rna/update_misc/genome.fa -t /mnt/data/liangjunmin/asm4_canu2.1/hap1_2/emboss/hap1_2/funannotate2/hap2/fun_rna/update_misc/trinity.fasta.clean -A -L --CPU 50 --annots /mnt/data/liangjunmin/asm4_canu2.1/hap1_2/emboss/hap1_2/funannotate2/hap2/fun_rna/update_misc/genome.gff3 [10/08/21 16:56:52]: CMD ERROR: /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/Launch_PASA_pipeline.pl -c /mnt/data/liangjunmin/asm4_canu2.1/hap1_2/emboss/hap1_2/funannotate2/hap2/fun_rna/update_misc/pasa/annotCompare.txt -g /mnt/data/liangjunmin/asm4_canu2.1/hap1_2/emboss/hap1_2/funannotate2/hap2/fun_rna/update_misc/genome.fa -t /mnt/data/liangjunmin/asm4_canu2.1/hap1_2/emboss/hap1_2/funannotate2/hap2/fun_rna/update_misc/trinity.fasta.clean -A -L --CPU 50 --annots /mnt/data/liangjunmin/asm4_canu2.1/hap1_2/emboss/hap1_2/funannotate2/hap2/fun_rna/update_misc/genome.gff3 [10/08/21 16:56:52]: -connecting to SQLite db: /mnt/data/liangjunmin/asm4_canu2.1/hap1_2/emboss/hap1_2/funannotate2/hap2/fun_rna/training/pasa/ustilago_maydis_pasa -*** Running PASA pipeine:

[Fri Oct 8 12:26:48 2021] Running CMD: /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/Load_Current_Gene_Annotations.dbi -c /mnt/data/liangjunmin/asm4_canu2.1/hap1_2/emboss/hap1_2/funannotate2/hap2/fun_rna/update_misc/pasa/annotCompare.txt -g /mnt/data/liangjunmin/asm4_canu2.1/hap1_2/emboss/hap1_2/funannotate2/hap2/fun_rna/update_misc/genome.fa -P /mnt/data/liangjunmin/asm4_canu2.1/hap1_2/emboss/hap1_2/funannotate2/hap2/fun_rna/update_misc/genome.gff3 > pasa_run.log.dir/output.annot_loading.39331.out

[Fri Oct 8 12:35:16 2021] Running CMD: /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/cDNA_annotation_comparer.dbi -G /mnt/data/liangjunmin/asm4_canu2.1/hap1_2/emboss/hap1_2/funannotate2/hap2/fun_rna/update_misc/genome.fa --CPU 50 -M '/mnt/data/liangjunmin/asm4_canu2.1/hap1_2/emboss/hap1_2/funannotate2/hap2/fun_rna/training/pasa/ustilago_maydis_pasa' > pasa_run.log.dir/ustilago_maydis_pasa.annotation_compare.39331.out Thread 1 terminated abnormally: Error, pasa binary [] isn't executable or couldn't be found. at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 66 thread 1. CDNA::PASA_alignment_assembler::_init(CDNA::PASA_alignment_assembler=HASH(0x7f760c6f4e20)) called at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 52 thread 1 CDNA::PASA_alignment_assembler::new("CDNA::PASA_alignment_assembler") called at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/cDNA_annotation_comparer.dbi line 1598 thread 1 main::get_alignment_assemblies_via_subcluster_id(DB_connect=HASH(0x55a83f9ed400), 1679, SCALAR(0x55a840a14490), HASH(0x55a840a0f138)) called at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/cDNA_annotation_comparer.dbi line 400 thread 1 main::process_contig("chromosome01B") called at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/cDNA_annotation_comparer.dbi line 311 thread 1 eval {...} called at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/cDNA_annotation_comparer.dbi line 311 thread 1 Thread 8 terminated abnormally: Error, pasa binary [] isn't executable or couldn't be found. at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 66 thread 8. CDNA::PASA_alignment_assembler::_init(CDNA::PASA_alignment_assembler=HASH(0x7f75cc68c908)) called at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/PerlLib/CDNA/PASA_alignment_assembler.pm line 52 thread 8 CDNA::PASA_alignment_assembler::new("CDNA::PASA_alignment_assembler") called at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/cDNA_annotation_comparer.dbi line 1598 thread 8 main::get_alignment_assemblies_via_subcluster_id(DB_connect=HASH(0x55a84459da70), 13169, SCALAR(0x55a8447d3280), HASH(0x55a8447cddd8)) called at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/cDNA_annotation_comparer.dbi line 400 thread 8 main::process_contig("chromosome08B") called at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/cDNA_annotation_comparer.dbi line 311 thread 8 eval {...} called at /data/Liangjunmin/opt/biosoft/miniconda3_for_pb-assembly/envs/funannotate/opt/pasa-2.4.1/scripts/cDNA_annotation_comparer.dbi line 311 thread 8

What command did you issue? I am using funannotate to annotate a fungal genome. The command was as: funannotate train -i genome -o fun --left --right funannotate predict -i genome -o fun --transcript_evidence trinity.fasta --rna_bam trinity.alignments.bam --cpus 50 funannotate update -i fun --cpus 50

Logfiles Please provide relavent log files of the error.

OS/Install Information

• output of funannotate check --show-versions 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)

[papelypluma]

Hi @jimie0311. I was wondering if by any chance you happen to address this issue? I'm also getting this issue with PASA.

Thank you very much.