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BEAV: Bacterial Element Annotation reVamped
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Failed to start bakta annotation #3

Open UpalabdhaD opened 3 months ago

UpalabdhaD commented 3 months ago

beav --input shivanshi_bakta_annotation/Plant_Pathogen/Pectobacterium_carotovorum/Pectobacterium_carotovorum.fna --output beav23/ --skip_tiger --bakta_arguments '--db $HOME/Shivanshi/shivanshi_bakta_annotation/db/ --force' BEAV version 1.0.0

--input shivanshi_bakta_annotation/Plant_Pathogen/Pectobacterium_carotovorum/Pectobacterium_carotovorum.fna --output beav23/ --skip_tiger --bakta_arguments --db $HOME/Shivanshi/shivanshi_bakta_annotation/db/ --force

Checking prerequisites:

Bakta: OK antiSMASH: OK MacSyFinder: OK IntegronFinder: OK DefenseFinder: OK TIGER2: skipped GapMind: OK DBSCAN-SWA: OK

Running Bakta

ERROR: wrong database path! --db=$HOME/Shivanshi/shivanshi_bakta_annotation/db/ Error: error occurred while running Bakta. Please see Bakta.log Elapsed: 0hrs 0min 1sec

Done

Annotation of other sequence elements

Traceback (most recent call last): File "/home2/upalabdha/test_beav/beav/share/beav-1.1.0/scripts/subset_cds_genbank.py", line 10, in for record in SeqIO.parse(f"./bakta/{strain}.gbff","gb"): File "/home2/upalabdha/test_beav/beav/lib/python3.9/site-packages/Bio/SeqIO/init.py", line 607, in parse return iterator_generator(handle) File "/home2/upalabdha/test_beav/beav/lib/python3.9/site-packages/Bio/SeqIO/InsdcIO.py", line 93, in init super().init(source, mode="t", fmt="GenBank") File "/home2/upalabdha/test_beav/beav/lib/python3.9/site-packages/Bio/SeqIO/Interfaces.py", line 47, in init self.stream = open(source, "r" + mode) FileNotFoundError: [Errno 2] No such file or directory: './bakta/Pectobacterium_carotovorum.gbff'

Error: Failed to open target sequence database bakta/Pectobacterium_carotovorum.fna for reading

Error: Failed to open target sequence database bakta/Pectobacterium_carotovorum.fna for reading

Error: Failed to open target sequence database bakta/Pectobacterium_carotovorum.fna for reading

mv: cannot stat './Pectobacterium_carotovorum.pip_box.out': No such file or directory mv: cannot stat './Pectobacterium_carotovorum.hrp_box.out': No such file or directory mv: cannot stat './Pectobacterium_carotovorum.nodbox': No such file or directory mv: cannot stat './Pectobacterium_carotovorum.ttsbox': No such file or directory mv: cannot stat './Pectobacterium_carotovorum.dif': No such file or directory cat: borders/Pectobacterium_carotovorum.nodbox: No such file or directory cat: borders/Pectobacterium_carotovorum.ttsbox: No such file or directory cat: borders/Pectobacterium_carotovorum.dif: No such file or directory

***** ERROR: Requested column 4, but database file - only has fields 1 - 0. cat: ./bakta/Pectobacterium_carotovorum.gff3: No such file or directory cut: ./borders/Pectobacterium_carotovorum.virbox: No such file or directory cut: ./borders/Pectobacterium_carotovorum.trabox: No such file or directory cut: ./borders/Pectobacterium_carotovorum.pip_box.out: No such file or directory cut: ./borders/Pectobacterium_carotovorum.hrp_box.out: No such file or directory Elapsed: 0hrs 0min 0sec

Done

Indentifying oriT

BLAST options error: File bakta/Pectobacterium_carotovorum.fna does not exist BLAST Database error: No alias or index file found for nucleotide database [bakta/Pectobacterium_carotovorum.fna] in search path [/home/upalabdha/Shivanshi/beav23/Pectobacterium_carotovorum::]

***** ERROR: Requested column 4, but database file - only has fields 1 - 0. rm: cannot remove 'bakta/Pectobacterium_carotovorum.fna.ndb': No such file or directory rm: cannot remove 'bakta/Pectobacterium_carotovorum.fna.nhr': No such file or directory rm: cannot remove 'bakta/Pectobacterium_carotovorum.fna.nin': No such file or directory rm: cannot remove 'bakta/Pectobacterium_carotovorum.fna.njs': No such file or directory rm: cannot remove 'bakta/Pectobacterium_carotovorum.fna.not': No such file or directory rm: cannot remove 'bakta/Pectobacterium_carotovorum.fna.nsq': No such file or directory rm: cannot remove 'bakta/Pectobacterium_carotovorum.fna.ntf': No such file or directory rm: cannot remove 'bakta/Pectobacterium_carotovorum.fna.nto': No such file or directory Elapsed: 0hrs 0min 0sec

Done

Identifying secretion systems (MacSyFinder)

macsyfinder: "No such model definition: 'TXSScan'" Error: error occurred while running MacSyFinder. Please see MacSyFinder.log Elapsed: 0hrs 0min 0sec cut: ./MacSyFinder_TXSS/best_solution.tsv: No such file or directory

Done

Identifying integrons (IntegronFinder)

usage: integron_finder [-h] [--local-max] [--func-annot] [--cpu CPU] [-dt DISTANCE_THRESHOLD] [--outdir OUTDIR] [--union-integrases] [--cmsearch CMSEARCH] [--hmmsearch HMMSEARCH] [--prodigal PRODIGAL] [--path-func-annot PATH_FUNC_ANNOT] [--gembase] [--gembase-path GEMBASE_PATH] [--annot-parser ANNOT_PARSER] [--prot-file PROT_FILE] [--attc-model ATTC_MODEL] [--evalue-attc EVALUE_ATTC] [--calin-threshold CALIN_THRESHOLD] [--keep-palindromes] [--no-proteins] [--promoter-attI] [--max-attc-size MAX_ATTC_SIZE] [--min-attc-size MIN_ATTC_SIZE] [--eagle-eyes] [--pdf] [--gbk] [--keep-tmp] [--split-results] [--circ | --linear] [--topology-file TOPOLOGY_FILE] [--version] [--mute] [-v] [-q] replicon integron_finder: error: argument replicon: ./bakta/Pectobacterium_carotovorum.fna no such file or directory Error: error occurred while running IntegronFinder. Please see Integron_Finder.log Elapsed: 0hrs 0min 1sec cut: ./Integron_Finder/Results_Integron_Finder_Pectobacterium_carotovorum/Pectobacterium_carotovorum.integrons: No such file or directory cat: ./Integron_Finder/Results_Integron_Finder_Pectobacterium_carotovorum/Pectobacterium_carotovorum.integrons: No such file or directory

Done

Identifying defense systems (DefenseFinder)

Error: error occurred while running DefenseFinder. Please see defensefinder.log Elapsed: 0hrs 0min 0sec cut: ./Pectobacterium_carotovorum_defense_finder_genes.tsv: No such file or directory

Done

Identifying biosynthetic gene clusters (antiSMASH)

usage: antismash [-h] [options ..] sequence antismash: error: Input file does not exist: Pectobacterium_carotovorum_cds_subset.gbk Error: error occurred while running antiSMASH Elapsed: 0hrs 0min 1sec Traceback (most recent call last): File "/home2/upalabdha/test_beav/beav/share/beav-1.1.0/scripts/antismash_genbanks_to_table.py", line 125, in main() File "/home2/upalabdha/test_beav/beav/share/beav-1.1.0/scripts/antismash_genbanks_to_table.py", line 85, in main df_bgcs = pd.concat(output, axis=0).sort_values(["genome_id", "contig_id", "start", "end"]) File "/home2/upalabdha/test_beav/beav/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 274, in concat op = _Concatenator( File "/home2/upalabdha/test_beav/beav/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 331, in init raise ValueError("No objects to concatenate") ValueError: No objects to concatenate

Done

Identifying phage (DBSCAN-SWA)

sed: can't read Pectobacterium_carotovorum_cds_subset.gbk: No such file or directory --2024-05-23 17:13:10-- http://www.microbiome-bigdata.com/PHISDetector/static/download/DBSCAN-SWA/db.tar.gz Connecting to 192.168.3.10:3128... connected. Proxy request sent, awaiting response... 403 Forbidden 2024-05-23 17:13:11 ERROR 403: Forbidden.

Error: error occurred while running DBSCAN-SWA. Please see dbscan-swa.log Elapsed: 0hrs 0min 3sec cut: ./DBSCAN-SWA/bac_DBSCAN-SWA_prophage_summary.txt: No such file or directory

Done

Characterizing amino acid biosynthesis and small carbon metabolite catabolism (GapMind)

GapMind: Running AA biosynthesis pathway analysis Can't locate DBI.pm in @INC (you may need to install the DBI module) (@INC contains: /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST/bin/../lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.36.0 /usr/local/share/perl/5.36.0 /usr/lib/x86_64-linux-gnu/perl5/5.36 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.36 /usr/share/perl/5.36 /usr/local/lib/site_perl) at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST/bin/../lib/FetchAssembly.pm line 14. BEGIN failed--compilation aborted at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST/bin/../lib/FetchAssembly.pm line 14. Compilation failed in require at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST//bin/buildorgs.pl line 7. BEGIN failed--compilation aborted at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST//bin/buildorgs.pl line 7. diamond v2.1.8.162 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

CPU threads: 16

Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) Database input file: GapMind/orgs.faa Opening the database file... Error opening file GapMind/orgs.faa: No such file or directory Can't locate DBI.pm in @INC (you may need to install the DBI module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.36.0 /usr/local/share/perl/5.36.0 /usr/lib/x86_64-linux-gnu/perl5/5.36 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.36 /usr/share/perl/5.36 /usr/local/lib/site_perl) at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST//bin/gapsearch.pl line 8. BEGIN failed--compilation aborted at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST//bin/gapsearch.pl line 8. No such file: GapMind/aa.hits Can't locate DBI.pm in @INC (you may need to install the DBI module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.36.0 /usr/local/share/perl/5.36.0 /usr/lib/x86_64-linux-gnu/perl5/5.36 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.36 /usr/share/perl/5.36 /usr/local/lib/site_perl) at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST//bin/gapsummary.pl line 7. BEGIN failed--compilation aborted at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST//bin/gapsummary.pl line 7. Can't locate DBI.pm in @INC (you may need to install the DBI module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.36.0 /usr/local/share/perl/5.36.0 /usr/lib/x86_64-linux-gnu/perl5/5.36 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.36 /usr/share/perl/5.36 /usr/local/lib/site_perl) at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST//bin/checkGapRequirements.pl line 5. BEGIN failed--compilation aborted at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST//bin/checkGapRequirements.pl line 5. awk: fatal: cannot open file GapMind/aa.sum.steps' for reading: No such file or directory GapMind: Running small molecule carbon catabolism analysis Can't locate DBI.pm in @INC (you may need to install the DBI module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.36.0 /usr/local/share/perl/5.36.0 /usr/lib/x86_64-linux-gnu/perl5/5.36 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.36 /usr/share/perl/5.36 /usr/local/lib/site_perl) at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST//bin/gapsearch.pl line 8. BEGIN failed--compilation aborted at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST//bin/gapsearch.pl line 8. No such file: GapMind/carbon.hits Can't locate DBI.pm in @INC (you may need to install the DBI module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.36.0 /usr/local/share/perl/5.36.0 /usr/lib/x86_64-linux-gnu/perl5/5.36 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.36 /usr/share/perl/5.36 /usr/local/lib/site_perl) at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST//bin/gapsummary.pl line 7. BEGIN failed--compilation aborted at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST//bin/gapsummary.pl line 7. Can't locate DBI.pm in @INC (you may need to install the DBI module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.36.0 /usr/local/share/perl/5.36.0 /usr/lib/x86_64-linux-gnu/perl5/5.36 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.36 /usr/share/perl/5.36 /usr/local/lib/site_perl) at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST//bin/checkGapRequirements.pl line 5. BEGIN failed--compilation aborted at /home2/upalabdha/test_beav/beav/share/beav-1.1.0/software/PaperBLAST//bin/checkGapRequirements.pl line 5. awk: fatal: cannot open fileGapMind/carbon.sum.steps' for reading: No such file or directory GapMind: Done mv: cannot stat 'formatdb.log': No such file or directory Elapsed: 0hrs 0min 3sec

Done

Identifying integrative conjugative elements [ICEs] (TIGER2)

Skipped

Combining annotations and preparing final output files Traceback (most recent call last): File "/home2/upalabdha/test_beav/beav/share/beav-1.1.0/scripts/combine_annotations.py", line 126, in for record in SeqIO.parse(f"./{strain}/bakta/{strain}.gbff","gb"): File "/home2/upalabdha/test_beav/beav/lib/python3.9/site-packages/Bio/SeqIO/init.py", line 607, in parse return iterator_generator(handle) File "/home2/upalabdha/test_beav/beav/lib/python3.9/site-packages/Bio/SeqIO/InsdcIO.py", line 93, in init super().init(source, mode="t", fmt="GenBank") File "/home2/upalabdha/test_beav/beav/lib/python3.9/site-packages/Bio/SeqIO/Interfaces.py", line 47, in init self.stream = open(source, "r" + mode) FileNotFoundError: [Errno 2] No such file or directory: './Pectobacterium_carotovorum/bakta/Pectobacterium_carotovorum.gbff' tee: Pectobacterium_carotovorum/logs/Beav.log: No such file or directory

Elapsed: 0hrs 0min 0sec No such file or directory Pectobacterium_carotovorum/Pectobacterium_carotovorum_final.gbk at /home2/upalabdha/test_beav/beav/bin/bp_genbank2gff3 line 422. cat: Pectobacterium_carotovorum/bakta/Pectobacterium_carotovorum.fna: No such file or directory

Final annotation output: Pectobacterium_carotovorum_final.gbk

Creating Circos Map

ls: cannot access 'beav23//Pectobacterium_carotovorum/_final.gbk': No such file or directory cat: 'beav23//Pectobacterium_carotovorum/oncogenic_plasmid_final.out.contiglist': No such file or directory python3 beav_circos.py --input usage: beav_circos.py [-h] --input INPUT [--contigs [CONTIGS ...]] [--plasmid PLASMID] beav_circos.py: error: argument --input/-i: expected one argument Elapsed: 0hrs 0min 0sec

Done mv: cannot stat 'Pectobacterium_carotovorum.circos.png': No such file or directory mv: cannot stat 'Pectobacterium_carotovorum.circos.pdf': No such file or directory mv: cannot stat 'Pectobacterium_carotovorum.oncogenes.png': No such file or directory mv: cannot stat 'Pectobacterium_carotovorum.oncogenes.pdf': No such file or directory mv: cannot stat 'Pectobacterium_carotovorum.oncogenic.gbk': No such file or directory

Summary of annotations

Secretion_Systems Defense_Systems Phages Biosynthetic_gene_clusters ICEs Integrons /home2/upalabdha/test_beav/beav/bin/beav: line 1064: N/A: No such file or directory N/A N/A 0 N/A N/A N/A

Small carbon catabolism pathways:

Done

The BEAV pipeline automates the use of a number of published software tools. If you use these results in a publication, please include the following in your methods section and cite:

Jung J, Rahman A, Schiffer A, and Weisberg A. 2023. BEAV: a bacterial genome and mobile element annotation pipeline. https://github.com/weisberglab/beav

grep: beav23//Pectobacterium_carotovorum/logs/bakta.log: No such file or directory Bakta version Schwengers O, Jelonek L, Dieckmann MA, et al. 2021. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom 7: 000685.

EMBOSS:fuzznuc EMBOSS: The European Molecular Biology Open Software Suite (2000) Rice,P. Longden,I. and Bleasby,A. Trends in Genetics 16, (6) pp276--277 head: cannot open 'beav23//Pectobacterium_carotovorum/MacSyFinder_TXSS/macsyfinder.log' for reading: No such file or directory MacSyFinder version Néron, Bertrand; Denise, Rémi; Coluzzi, Charles; Touchon, Marie; Rocha, Eduardo P.C.; Abby, SophieS 2023. MacSyFinder v2: Improved modelling and search engine to identify molecular systems igenomes. Peer Community Journal, Volume 3, article no. e28. DOI: 10.24072/pcjournal.250.

DBSCAN-SWA Gan R, Zhou F, Si Y, et al. 2022. DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation. Frontiers in Genetics 13.

DefenseFinder Tesson F., Hervé A. , Touchon M., d’Humières C., Cury J., Bernheim A. Systematic and quantitative view of the antiviral arsenal of prokaryotes bioRx

grep: beav23//Pectobacterium_carotovorum/Integron_Finder/Results_Integron_Finder_Pectobacterium_carotovorum/integron_finder.out: No such file or directory IntegronFinder version Néron B, Littner E, Haudiquet M, et al. 2022. IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella. Microorganisms 10: 700.

grep: beav23//Pectobacterium_carotovorum/antiSMASH/index.html: No such file or directory antiSMASH version Kai Blin, Simon Shaw, Alexander M Kloosterman, Zach Charlop-Powers, Gilles P van Weezel, Marnix H Medema, & Tilmann Weber. 2021. Nucleic Acids Research DOI:10.1093/nar/gkab335.

GapMind Amino acid biosynthesis: Price MN, Deutschbauer AM, and Arkin AP. 2020. GapMind: Automated Annotation of Amino Acid Biosynthesis. mSystems 5: e00291-20. Catabolic pathways: Price MN, Deutschbauer AM, and Arkin AP. 2022. Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics. PLOS Genetics 18(4): e1010156. DOI:10.1371/journal.pgen.1010156

acarafat commented 3 months ago

Thanks for reporting the issue. Can you also share the Bakta.log?