benyoung93
commented
11 months ago been doing a little more sleuthing through log files.
In the funannotate-annotate.bf6cb020.log it shows the XML command that is being run
/nethome/bdy8/mambaforge/envs/funannotate_env/bin/python /nethome/bdy8/mambaforge/envs/funannotate_env/lib/python3.8/site-packages/funannotate/aux_scripts/iprscan2annotations.py /scratch/projects/omics/ofav_genome/funannotate/step_5_predict/annotate_misc/iprscan.xml /scratch/projects/omics/ofav_genome/funannotate/step_5_predict/annotate_misc/annotations.iprscan.txtSo interestingly i went to look at the annotations.iprscan.txt that the output should be written to for this step, and the file is not empty.
with a head
Ofa_008232-T1 db_xref InterPro:IPR003968
Ofa_008232-T1 db_xref InterPro:IPR003972
Ofa_008232-T1 db_xref InterPro:IPR000210
Ofa_008232-T1 db_xref InterPro:IPR005821
Ofa_008232-T1 db_xref InterPro:IPR027359
Ofa_008232-T1 db_xref InterPro:IPR003131
Ofa_008232-T1 db_xref InterPro:IPR011333
Ofa_008232-T1 db_xref InterPro:IPR028325
Ofa_008232-T1 go_process potassium ion transport|0006813||IEA
Ofa_008232-T1 go_function channel activity|0015267||IEAand a wc -l of the file shows 535494 lines.
So I am even more stumped now as to why it is not completing past this step. Maybe it is the last line in the XML file ?? Here is a tail -20 of the xml file just in case.
</panther-location>
</locations>
</panther-match>
<superfamilyhmmer3-match evalue="5.33E-15">
<signature ac="SSF50978" name="WD40 repeat-like">
<entry ac="IPR036322" desc="WD40-repeat-containing domain superfamily" name="WD40_repeat_dom_sf" type="HOMOLOGOUS_SUPERFAMILY"/>
<signature-library-release library="SUPERFAMILY" version="1.75"/>
</signature>
<model-ac>0049784</model-ac>
<locations>
<superfamilyhmmer3-location hmm-length="340" start="12" end="167">
<location-fragments>
<superfamilyhmmer3-location-fragment start="12" end="167" dc-status="CONTINUOUS"/>
</location-fragments>
</superfamilyhmmer3-location>
</locations>
</superfamilyhmmer3-match>
</matches>
</protein>
</protein-matches>
nextgenusfs
Are you using the latest release? Yep :)
Describe the bug I get the following error message (in logfile section below) when running the annotate step, it is linked to the XML file from InterproScan that I ran locally. Version of interproscan is
Here is a
head -20of the xml file from interproscan. I used theproteins.fafromfunannotate updateas inpur for interproscan.Here is a
grep ">" proteins.fa | head -20of the proteins fasta from the update command.and a
head .gff3fromfunannotae::updateWhat command did you issue?
Logfiles To try and be a wee bit more concise did not put the whole log file in, just a few lines above where the error comes in in my LSF .err file
and here is the entirety of the log file from the annotate command. I notice I was stupid and need to reset the busco, will do that in a later run once this error is fixed.
OS/Install Information
funannotate check --show-versionsYou are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.50 Clone: 0.46 DBD::SQLite: 1.72 DBD::mysql: 4.046 DBI: 1.643 DB_File: 1.858 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.54 Hash::Merge: 0.302 JSON: 4.10 LWP::UserAgent: 6.67 Logger::Simple: 2.0 POSIX: 1.94 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.14 Tie::File: 1.06 URI::Escape: 5.17 YAML: 1.30 local::lib: 2.000029 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed
Checking Environmental Variables... $FUNANNOTATE_DB=/scratch/projects/omics/ofav_genome/funannotate_db $PASAHOME=/nethome/bdy8/mambaforge/envs/funannotate_env/opt/pasa-2.5.2 $TRINITY_HOME=/nethome/bdy8/mambaforge/envs/funannotate_env/opt/trinity-2.8.5 $EVM_HOME=/nethome/bdy8/mambaforge/envs/funannotate_env/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/nethome/bdy8/mambaforge/envs/funannotate_env/config/ $GENEMARK_PATH=/nethome/bdy8/mambaforge/envs/funannotate_env/opt/gmes_linux_64 All 6 environmental variables are set
Checking external dependencies... PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.5.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.31.0 blat: BLAT v37x1 diamond: 2.1.7 emapper.py: 2.1.11 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: 36.3.8g glimmerhmm: 3.0.4 gmap: 2023-04-28 hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 17.0.3-internal kallisto: 0.46.1 mafft: v7.520 (2023/Mar/22) makeblastdb: makeblastdb 2.14.0+ minimap2: 2.26-r1175 pigz: 2.6 proteinortho: 6.2.3 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.16.1 snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.6 (May 2020) tantan: tantan 40 tbl2asn: 25.8 tblastn: tblastn 2.14.0+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 ERROR: gmes_petap.pl not installed ERROR: signalp not installed