prokka
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Published
20 hours ago •
tseemann
tseemann
Prokka empty and temporary output files
Hi,
I downloaded prokka using conda and am running it with a custom database (PHROGs: https://phrogs.lmge.uca.fr/) to annotate prokaryotic viruses. I am doing this on my university's HPC using a for loop. It seems to work fine for most (3930) of my files, but seems to be malfunctioning for a small (5) handful. Specifically, for this small handful, prokka runs through these files with no error, but creates empty outputs (.faa, etc.). It also never deletes several temporary files.
I've double checked the input .fasta files which lead to these empty outputs and they all look fine. Each is a standard .fasta (header starting with ">") which is readable, non-zero, and most definitely a file. They all also have one sequence per file and are fairly short (~5-10kb).
One of the problemed files: busby_phage_123.fa
The loop I run:
for f in *.fa
do
sbatch ../scripts/annot.sh $f
done
The code portion of annot.sh
conda activate prokka
prokka --kingdom Bacteria $1 \
--outdir ~bee_phage/dls/network/annot/${1%%.fa} \
--hmms ~/phrogs/all_phrogs.hmm \
--prefix annotate_${1%%.fa}
Output dir:
-rw-rw-r-- 1 dsbard dsbard 0 Jun 28 14:52 annotate_busby_phage_123.AMR.tmp.588077.faa
-rw-rw-r-- 1 dsbard dsbard 0 Jun 28 14:52 annotate_busby_phage_123.HAMAP.hmm.tmp.588077.faa
-rw-rw-r-- 1 dsbard dsbard 0 Jun 28 14:52 annotate_busby_phage_123.IS.tmp.588077.faa
-rw-rw-r-- 1 dsbard dsbard 0 Jun 28 14:52 annotate_busby_phage_123.all_phrogs.hmm.tmp.588077.faa
-rw-rw-r-- 1 dsbard dsbard 3.1K Jun 28 14:52 annotate_busby_phage_123.err
-rw-rw-r-- 1 dsbard dsbard 0 Jun 28 14:52 annotate_busby_phage_123.faa
-rw-rw-r-- 1 dsbard dsbard 0 Jun 28 14:52 annotate_busby_phage_123.ffn
-rw-rw-r-- 1 dsbard dsbard 1.9K Jun 28 14:52 annotate_busby_phage_123.fna
-rw-rw-r-- 1 dsbard dsbard 2.0K Jun 28 14:52 annotate_busby_phage_123.fsa
-rw-rw-r-- 1 dsbard dsbard 2.9K Jun 28 14:52 annotate_busby_phage_123.gbk
-rw-rw-r-- 1 dsbard dsbard 2.0K Jun 28 14:52 annotate_busby_phage_123.gff
-rw-rw-r-- 1 dsbard dsbard 8.6K Jun 28 14:52 annotate_busby_phage_123.log
-rw-rw-r-- 1 dsbard dsbard 0 Jun 28 14:52 annotate_busby_phage_123.sprot.tmp.588077.faa
-rw-rw-r-- 1 dsbard dsbard 3.0K Jun 28 14:52 annotate_busby_phage_123.sqn
-rw-rw-r-- 1 dsbard dsbard 25 Jun 28 14:52 annotate_busby_phage_123.tbl
-rw-rw-r-- 1 dsbard dsbard 53 Jun 28 14:52 annotate_busby_phage_123.tsv
-rw-rw-r-- 1 dsbard dsbard 55 Jun 28 14:52 annotate_busby_phage_123.txt
Log file contents:
[14:52:04] This is prokka 1.14.6
[14:52:04] Written by Torsten Seemann <[email protected]>
[14:52:04] Homepage is https://github.com/tseemann/prokka
[14:52:04] Local time is Wed Jun 28 14:52:04 2023
[14:52:04] You are dsbard
[14:52:04] Operating system is linux
[14:52:04] You have BioPerl 1.7.8
[14:52:04] System has 24 cores.
[14:52:04] Will use maximum of 8 cores.
[14:52:04] Annotating as >>> Bacteria <<<
[14:52:04] Generating locus_tag from 'busby_phage_123.fa' contents.
[14:52:04] Setting --locustag ELNPBALK from MD5 e579ba5461c138c2561e1d09ab83f040
[14:52:04] Creating new output folder: /home/dsbard/bee_phage/dls/network/annot/busby_phage_123
[14:52:04] Running: mkdir -p \/home\/dsbard\/bee_phage\/dls\/network\/annot\/busby_phage_123
[14:52:04] Using filename prefix: annotate_busby_phage_123.XXX
[14:52:04] Setting HMMER_NCPU=1
[14:52:04] Writing log to: /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.log
[14:52:04] Command: /home/dsbard/yes/envs/prokka/bin/prokka --kingdom Bacteria busby_phage_123.fa --outdir /home/dsbard/bee_phage/dls/network/annot/busby_phage_123 --hmms /home/dsbard/phrogs/all_phrogs.hmm --prefix annotate_busby_phage_123
[14:52:04] Appending to PATH: /home/dsbard/yes/envs/prokka/bin
[14:52:04] Looking for 'aragorn' - found /home/dsbard/yes/envs/prokka/bin/aragorn
[14:52:04] Determined aragorn version is 001002 from 'ARAGORN v1.2.41 Dean Laslett'
[14:52:04] Looking for 'barrnap' - found /home/dsbard/yes/envs/prokka/bin/barrnap
[14:52:04] Determined barrnap version is 000009 from 'barrnap 0.9'
[14:52:04] Looking for 'blastp' - found /home/dsbard/yes/envs/prokka/bin/blastp
[14:52:04] Determined blastp version is 002014 from 'blastp: 2.14.0+'
[14:52:04] Looking for 'cmpress' - found /home/dsbard/yes/envs/prokka/bin/cmpress
[14:52:04] Determined cmpress version is 001001 from '# INFERNAL 1.1.4 (Dec 2020)'
[14:52:04] Looking for 'cmscan' - found /home/dsbard/yes/envs/prokka/bin/cmscan
[14:52:05] Determined cmscan version is 001001 from '# INFERNAL 1.1.4 (Dec 2020)'
[14:52:05] Looking for 'egrep' - found /usr/bin/egrep
[14:52:05] Looking for 'find' - found /usr/bin/find
[14:52:05] Looking for 'grep' - found /usr/bin/grep
[14:52:05] Looking for 'hmmpress' - found /home/dsbard/yes/envs/prokka/bin/hmmpress
[14:52:05] Determined hmmpress version is 003003 from '# HMMER 3.3.2 (Nov 2020); http://hmmer.org/'
[14:52:05] Looking for 'hmmscan' - found /home/dsbard/yes/envs/prokka/bin/hmmscan
[14:52:05] Determined hmmscan version is 003003 from '# HMMER 3.3.2 (Nov 2020); http://hmmer.org/'
[14:52:05] Looking for 'java' - found /home/dsbard/yes/envs/prokka/bin/java
[14:52:05] Looking for 'makeblastdb' - found /home/dsbard/yes/envs/prokka/bin/makeblastdb
[14:52:05] Determined makeblastdb version is 002014 from 'makeblastdb: 2.14.0+'
[14:52:05] Looking for 'minced' - found /home/dsbard/yes/envs/prokka/bin/minced
[14:52:05] Determined minced version is 004002 from 'minced 0.4.2'
[14:52:05] Looking for 'parallel' - found /home/dsbard/yes/envs/prokka/bin/parallel
[14:52:05] Determined parallel version is 20230522 from 'GNU parallel 20230522'
[14:52:05] Looking for 'prodigal' - found /home/dsbard/yes/envs/prokka/bin/prodigal
[14:52:05] Determined prodigal version is 002006 from 'Prodigal V2.6.3: February, 2016'
[14:52:05] Looking for 'prokka-genbank_to_fasta_db' - found /home/dsbard/yes/envs/prokka/bin/prokka-genbank_to_fasta_db
[14:52:05] Looking for 'sed' - found /usr/bin/sed
[14:52:05] Looking for 'tbl2asn' - found /home/dsbard/yes/envs/prokka/bin/tbl2asn
[14:52:05] Determined tbl2asn version is 025007 from 'tbl2asn 25.7 arguments:'
[14:52:05] Using genetic code table 11.
[14:52:05] Loading and checking input file: busby_phage_123.fa
[14:52:05] Wrote 1 contigs totalling 1857 bp.
[14:52:05] Predicting tRNAs and tmRNAs
[14:52:05] Running: aragorn -l -gc11 -w \/home\/dsbard\/bee_phage\/dls\/network\/annot\/busby_phage_123\/annotate_busby_phage_123\.fna
[14:52:06] Found 0 tRNAs
[14:52:06] Predicting Ribosomal RNAs
[14:52:06] Running Barrnap with 8 threads
[14:52:06] Found 0 rRNAs
[14:52:06] Skipping ncRNA search, enable with --rfam if desired.
[14:52:06] Total of 0 tRNA + rRNA features
[14:52:06] Searching for CRISPR repeats
[14:52:06] Found 0 CRISPRs
[14:52:06] Predicting coding sequences
[14:52:06] Contigs total 1857 bp, so using meta mode
[14:52:06] Running: prodigal -i \/home\/dsbard\/bee_phage\/dls\/network\/annot\/busby_phage_123\/annotate_busby_phage_123\.fna -c -m -g 11 -p meta -f sco -q
[14:52:06] Found 0 CDS
[14:52:06] Connecting features back to sequences
[14:52:06] Not using genus-specific database. Try --usegenus to enable it.
[14:52:06] Preparing user-supplied primary HMMER annotation source: /home/dsbard/phrogs/all_phrogs.hmm
[14:52:06] Using /inference source as 'all_phrogs'
[14:52:06] Annotating CDS, please be patient.
[14:52:06] Will use 8 CPUs for similarity searching.
[14:52:06] Found 0 unique /gene codes.
[14:52:06] Fixed 0 colliding /gene names.
[14:52:06] Adding /locus_tag identifiers
[14:52:06] Assigned 0 locus_tags to CDS and RNA features.
[14:52:06] Writing outputs to /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/
[14:52:06] Generating annotation statistics file
[14:52:06] Generating Genbank and Sequin files
[14:52:06] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.6 from https://github.com/tseemann/prokka' -Z \/home\/dsbard\/bee_phage\/dls\/network\/annot\/busby_phage_123\/annotate_busby_phage_123\.err -i \/home\/dsbard\/bee_phage\/dls\/network\/annot\/busby_phage_123\/annotate_busby_phage_123\.fsa 2> /dev/null
[14:52:07] Deleting unwanted file: /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/errorsummary.val
[14:52:07] Deleting unwanted file: /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.dr
[14:52:07] Deleting unwanted file: /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.fixedproducts
[14:52:07] Deleting unwanted file: /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.ecn
[14:52:07] Deleting unwanted file: /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.val
[14:52:07] Repairing broken .GBK output that tbl2asn produces...
[14:52:07] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/home\/dsbard\/bee_phage\/dls\/network\/annot\/busby_phage_123\/annotate_busby_phage_123\.gbf > \/home\/dsbard\/bee_phage\/dls\/network\/annot\/busby_phage_123\/annotate_busby_phage_123\.gbk
[14:52:07] Deleting unwanted file: /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.gbf
[14:52:07] Output files:
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.ffn
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.tbl
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.faa
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.sqn
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.all_phrogs.hmm.tmp.588077.faa
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.IS.tmp.588077.faa
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.gbk
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.tsv
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.sprot.tmp.588077.faa
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.txt
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.fsa
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.AMR.tmp.588077.faa
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.fna
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.gff
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.err
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.HAMAP.hmm.tmp.588077.faa
[14:52:07] /home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123.log
[14:52:07] Annotation finished successfully.
[14:52:07] Walltime used: 0.05 minutes
[14:52:07] If you use this result please cite the Prokka paper:
[14:52:07] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
[14:52:07] Type 'prokka --citation' for more details.
[14:52:07] Share and enjoy!
Error file contents
Discrepancy Report Results
Summary
DISC_SOURCE_QUALS_ASNDISC:strain (all present, all unique)
DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all unique)
DISC_COUNT_NUCLEOTIDES:1 nucleotide Bioseqs are present
NO_ANNOTATION:1 bioseqs have no features
DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
ONCALLER_COMMENT_PRESENT:1 comment descriptors were found (all same)
MISSING_GENOMEASSEMBLY_COMMENTS:1 bioseqs are missing GenomeAssembly structured comments
MOLTYPE_NOT_MRNA:1 molecule types are not set as mRNA.
TECHNIQUE_NOT_TSA:1 technique are not set as TSA
MISSING_STRUCTURED_COMMENT:1 sequences do not include structured comments.
MISSING_PROJECT:1 sequences do not include project.
DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
Detailed Report
DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all unique)
DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::1 sources have unique values for strain
DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all unique)
DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::1 sources have unique values for taxname
DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::1 nucleotide Bioseqs are present
/home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123:busby_phage_123 (length 1857)
DiscRep_ALL:NO_ANNOTATION::1 bioseqs have no features
/home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123:busby_phage_123 (length 1857)
DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.
DiscRep_ALL:ONCALLER_COMMENT_PRESENT::1 comment descriptors were found (all same)
/home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123:busby_phage_123:Annotated using prokka 1.14.6 from https://github.com/tseemann/prokka
DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::1 bioseqs are missing GenomeAssembly structured comments
/home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123:busby_phage_123 (length 1857)
DiscRep_ALL:MOLTYPE_NOT_MRNA::1 molecule types are not set as mRNA.
/home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123:busby_phage_123 (length 1857)
DiscRep_ALL:TECHNIQUE_NOT_TSA::1 technique are not set as TSA
/home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123:busby_phage_123 (length 1857)
DiscRep_ALL:MISSING_STRUCTURED_COMMENT::1 sequences do not include structured comments.
/home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123:busby_phage_123 (length 1857)
DiscRep_ALL:MISSING_PROJECT::1 sequences do not include project.
/home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123:busby_phage_123 (length 1857)
DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)
DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::1 Molinfos are missing field technique
/home/dsbard/bee_phage/dls/network/annot/busby_phage_123/annotate_busby_phage_123:busby_phage_123 (length 1857)
And finally, the contents of my conda env:
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alsa-lib 1.2.8 h166bdaf_0 conda-forge
aragorn 1.2.41 h031d066_1 bioconda
barrnap 0.9 hdfd78af_4 bioconda
bedtools 2.31.0 hf5e1c6e_2 bioconda
blast 2.14.0 h7d5a4b4_1 bioconda
boost 1.67.0 py37_4
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.19.1 hd590300_0 conda-forge
ca-certificates 2023.5.7 hbcca054_0 conda-forge
clustalw 2.1 h4ac6f70_9 bioconda
curl 7.88.1 h5eee18b_0
entrez-direct 16.2 he881be0_1 bioconda
expat 2.5.0 hcb278e6_1 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.12.1 hca18f0e_1 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
giflib 5.2.1 h0b41bf4_3 conda-forge
gmp 6.1.2 hf484d3e_1000 conda-forge
gnutls 3.5.19 h2a4e5f8_1 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
hmmer 3.3.2 hdbdd923_4 bioconda
icu 58.2 hf484d3e_1000 conda-forge
infernal 1.1.4 pl5321h031d066_4 bioconda
krb5 1.19.4 h568e23c_0
lcms2 2.15 haa2dc70_1 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libblas 3.9.0 17_linux64_openblas conda-forge
libboost 1.67.0 h46d08c1_4
libcblas 3.9.0 17_linux64_openblas conda-forge
libcups 2.3.3 h3e49a29_2 conda-forge
libcurl 7.88.1 h91b91d3_0
libdb 6.2.32 h9c3ff4c_0 conda-forge
libdeflate 1.18 h0b41bf4_0 conda-forge
libedit 3.1.20221030 h5eee18b_0
libev 4.33 h516909a_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.1.0 he5830b7_0 conda-forge
libgfortran-ng 13.1.0 h69a702a_0 conda-forge
libgfortran5 13.1.0 h15d22d2_0 conda-forge
libglib 2.76.3 hebfc3b9_0 conda-forge
libgomp 13.1.0 he5830b7_0 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libidn11 1.34 h1cef754_0 conda-forge
libidn2 2.3.4 h166bdaf_0 conda-forge
libjpeg-turbo 2.1.5.1 h0b41bf4_0 conda-forge
liblapack 3.9.0 17_linux64_openblas conda-forge
libnghttp2 1.46.0 hce63b2e_0
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.23 pthreads_h80387f5_0 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libsqlite 3.42.0 h2797004_0 conda-forge
libssh2 1.10.0 h8f2d780_0
libstdcxx-ng 13.1.0 hfd8a6a1_0 conda-forge
libtiff 4.5.0 ha587672_6 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.3.0 h0b41bf4_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
minced 0.4.2 hdfd78af_1 bioconda
ncurses 6.4 hcb278e6_0 conda-forge
nettle 3.3 0 conda-forge
numpy 1.21.6 py37h976b520_0 conda-forge
openjdk 11.0.1 h516909a_1016 conda-forge
openssl 1.1.1u hd590300_0 conda-forge
paml 4.10.6 h031d066_2 bioconda
parallel 20230522 ha770c72_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.40 hc3806b6_0 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
perl-algorithm-diff 1.1903 pl5321hdfd78af_3 bioconda
perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda
perl-base 2.23 pl5321hdfd78af_2 bioconda
perl-bio-asn1-entrezgene 1.73 pl5321hdfd78af_3 bioconda
perl-bio-coordinate 1.007001 pl5321hdfd78af_3 bioconda
perl-bio-featureio 1.6.905 pl5321hdfd78af_4 bioconda
perl-bio-samtools 1.43 pl5321he4a0461_4 bioconda
perl-bio-searchio-hmmer 1.7.3 pl5321hdfd78af_0 bioconda
perl-bio-tools-phylo-paml 1.7.3 pl5321hdfd78af_3 bioconda
perl-bio-tools-run-alignment-clustalw 1.7.4 pl5321hdfd78af_3 bioconda
perl-bio-tools-run-alignment-tcoffee 1.7.4 pl5321hdfd78af_4 bioconda
perl-bioperl 1.7.8 hdfd78af_1 bioconda
perl-bioperl-core 1.7.8 pl5321hdfd78af_1 bioconda
perl-bioperl-run 1.007003 pl5321hdfd78af_0 bioconda
perl-business-isbn 3.007 pl5321hdfd78af_0 bioconda
perl-business-isbn-data 20210112.006 pl5321hdfd78af_0 bioconda
perl-capture-tiny 0.48 pl5321hdfd78af_2 bioconda
perl-carp 1.38 pl5321hdfd78af_4 bioconda
perl-class-data-inheritable 0.09 pl5321hdfd78af_0 bioconda
perl-common-sense 3.75 pl5321hdfd78af_0 bioconda
perl-compress-raw-bzip2 2.201 pl5321h87f3376_1 bioconda
perl-compress-raw-zlib 2.105 pl5321h87f3376_0 bioconda
perl-constant 1.33 pl5321hdfd78af_2 bioconda
perl-data-dumper 2.183 pl5321hec16e2b_1 bioconda
perl-db_file 1.858 pl5321h166bdaf_0 conda-forge
perl-devel-stacktrace 2.04 pl5321hdfd78af_1 bioconda
perl-digest-hmac 1.04 pl5321hdfd78af_0 bioconda
perl-digest-md5 2.58 pl5321hec16e2b_1 bioconda
perl-encode 3.19 pl5321hec16e2b_1 bioconda
perl-encode-locale 1.05 pl5321hdfd78af_7 bioconda
perl-exception-class 1.45 pl5321hdfd78af_0 bioconda
perl-exporter 5.72 pl5321hdfd78af_2 bioconda
perl-exporter-tiny 1.002002 pl5321hdfd78af_0 bioconda
perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge
perl-file-listing 6.15 pl5321hdfd78af_0 bioconda
perl-file-path 2.18 pl5321hd8ed1ab_0 conda-forge
perl-file-slurp-tiny 0.004 pl5321hdfd78af_2 bioconda
perl-file-sort 1.01 pl5321hdfd78af_3 bioconda
perl-file-spec 3.48_01 pl5321hdfd78af_2 bioconda
perl-file-temp 0.2304 pl5321hd8ed1ab_0 conda-forge
perl-getopt-long 2.54 pl5321hdfd78af_0 bioconda
perl-html-parser 3.81 pl5321h4ac6f70_1 bioconda
perl-html-tagset 3.20 pl5321hdfd78af_4 bioconda
perl-http-cookies 6.10 pl5321hdfd78af_0 bioconda
perl-http-daemon 6.16 pl5321hdfd78af_0 bioconda
perl-http-date 6.05 pl5321hdfd78af_0 bioconda
perl-http-message 6.36 pl5321hdfd78af_0 bioconda
perl-http-negotiate 6.01 pl5321hdfd78af_4 bioconda
perl-inc-latest 0.500 pl5321ha770c72_0 conda-forge
perl-io-compress 2.201 pl5321hdbdd923_2 bioconda
perl-io-html 1.004 pl5321hdfd78af_0 bioconda
perl-io-socket-ssl 2.074 pl5321hdfd78af_0 bioconda
perl-io-string 1.08 pl5321hdfd78af_4 bioconda
perl-io-tty 1.16 pl5321hec16e2b_1 bioconda
perl-io-zlib 1.14 pl5321hdfd78af_0 bioconda
perl-ipc-run 20200505.0 pl5321hdfd78af_0 bioconda
perl-json 4.10 pl5321hdfd78af_0 bioconda
perl-json-xs 2.34 pl5321h4ac6f70_6 bioconda
perl-libwww-perl 6.67 pl5321hdfd78af_0 bioconda
perl-libxml-perl 0.08 pl5321hdfd78af_3 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h031d066_2 bioconda
perl-lwp-mediatypes 6.04 pl5321hdfd78af_1 bioconda
perl-mime-base64 3.16 pl5321hec16e2b_2 bioconda
perl-module-build 0.4234 pl5321ha770c72_0 conda-forge
perl-net-http 6.22 pl5321hdfd78af_0 bioconda
perl-net-ssleay 1.92 pl5321h0e0aaa8_1 bioconda
perl-ntlm 1.09 pl5321hdfd78af_5 bioconda
perl-parent 0.236 pl5321hdfd78af_2 bioconda
perl-pathtools 3.75 pl5321hec16e2b_3 bioconda
perl-scalar-list-utils 1.62 pl5321hec16e2b_1 bioconda
perl-socket 2.027 pl5321h031d066_4 bioconda
perl-sub-uplevel 0.2800 pl5321hec16e2b_4 bioconda
perl-test-deep 1.130 pl5321hdfd78af_0 bioconda
perl-test-differences 0.69 pl5321hdfd78af_0 bioconda
perl-test-exception 0.43 pl5321hdfd78af_3 bioconda
perl-test-most 0.38 pl5321hdfd78af_0 bioconda
perl-test-warn 0.36 pl5321hdfd78af_2 bioconda
perl-text-diff 1.45 pl5321hdfd78af_1 bioconda
perl-time-local 1.35 pl5321hdfd78af_0 bioconda
perl-timedate 2.33 pl5321hdfd78af_2 bioconda
perl-tree-dag_node 1.32 pl5321hdfd78af_0 bioconda
perl-try-tiny 0.31 pl5321hdfd78af_1 bioconda
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
perl-uri 5.12 pl5321hdfd78af_0 bioconda
perl-url-encode 0.03 pl5321h9ee0642_0 bioconda
perl-www-robotrules 6.02 pl5321hdfd78af_4 bioconda
perl-xml-dom 1.46 pl5321hdfd78af_1 bioconda
perl-xml-dom-xpath 0.14 pl5321hdfd78af_2 bioconda
perl-xml-namespacesupport 1.12 pl5321hdfd78af_1 bioconda
perl-xml-parser 2.44_01 pl5321hc3e0081_1003 conda-forge
perl-xml-regexp 0.04 pl5321hdfd78af_3 bioconda
perl-xml-sax 1.02 pl5321hdfd78af_1 bioconda
perl-xml-sax-base 1.09 pl5321hdfd78af_1 bioconda
perl-xml-sax-expat 0.51 pl5321hdfd78af_4 bioconda
perl-xml-simple 2.25 pl5321hdfd78af_2 bioconda
perl-xml-xpathengine 0.14 pl5321hdfd78af_3 bioconda
pip 23.1.2 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
prodigal 2.6.3 h031d066_6 bioconda
prokka 1.14.6 pl5321hdfd78af_4 bioconda
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
py-boost 1.67.0 py37h04863e7_4
python 3.7.12 hb7a2778_100_cpython conda-forge
python_abi 3.7 3_cp37m conda-forge
readline 8.2 h8228510_1 conda-forge
setuptools 67.7.2 pyhd8ed1ab_0 conda-forge
sqlite 3.42.0 h2c6b66d_0 conda-forge
t_coffee 11.0.8 py37hea885bf_8 bioconda
tbl2asn-forever 25.7.2f h031d066_4 bioconda
tk 8.6.12 h27826a3_0 conda-forge
wget 1.20.3 ha56f1ee_1 conda-forge
wheel 0.40.0 pyhd8ed1ab_0 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.5 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.13 h166bdaf_4 conda-forge
zstd 1.5.2 h3eb15da_6 conda-forge
Its my first time making one of these issues, so let me know if there is some other info I should have included. Any help would be greatly appreciated! Thank you.
