iprscan.xml related erro

Panda-smile commented 3 months ago

Are you using the latest release? 1.8.17

Describe the bug Content does not exist in xml file，The xml file has been submitted and modified to txt suffix iprscan.txt

What command did you issue? Singularity> funannotate iprscan -i /data/FQ2mix_MF_alive -c 32 usage: funannotate-iprscan.py [-h] -i INPUT [-n NUM] [-c CPUS] -m {local,docker} [--cpus_per_chunk CPUS_PER_CHUNK] [--iprscan_path IPRSCAN_PATH] [-o OUT] [--debug] [--no-progress] funannotate-iprscan.py: error: the following arguments are required: -m/--method Singularity> funannotate iprscan -i /data/FQ2mix_MF_alive -c 32 -m local Running InterProScan5 on 11021 proteins Important: you need to manually configure your interproscan.properties file for embedded workers. Will try to launch 32 interproscan processes, adjust -c,--cpus for your system Progress: 11 complete, 0 failed, 0 remaining
InterProScan5 search has completed successfully! Results are here: /data/FQ2mix_MF_alive/annotate_misc/iprscan.xml

Logfiles Run InterProScan (manual install): funannotate iprscan -i /data/FQ2mix_MF_alive -c 32

Run antiSMASH (optional): funannotate remote -i /data/FQ2mix_MF_alive -m antismash -e youremail@server.edu

Annotate Genome: funannotate annotate -i /data/FQ2mix_MF_alive --cpus 32 --sbt yourSBTfile.txt

[03/20/24 23:33:29]: Training parameters file saved: /data/FQ2mix_MF_alive/predict_results/millerozyma_farinosa_fq2minimf.parameters.json [03/20/24 23:33:29]: Add species parameters to database:

funannotate species -s millerozyma_farinosa_fq2minimf -a /data/FQ2mix_MF_alive/predict_results/millerozyma_farinosa_fq2minimf.parameters.json

OS/Install Information

output of funannotate check --show-versions Singularity> funannotate check --show-versions

Checking dependencies for 1.8.17

You are running Python v 3.8.12. Now checking python packages... biopython: 1.76 goatools: 1.3.11 matplotlib: 3.7.3 natsort: 8.4.0 numpy: 1.22.4 pandas: 2.0.3 psutil: 5.7.0 requests: 2.31.0 scikit-learn: 0.24.2 scipy: 1.5.3 seaborn: 0.13.0 All 11 python packages installed

You are running Perl v b'5.026002'. Now checking perl modules... Carp: 1.38 Clone: 0.42 DBD::SQLite: 1.64 DBD::mysql: 4.046 DBI: 1.642 DB_File: 1.855 Data::Dumper: 2.173 File::Basename: 2.85 File::Which: 1.23 Getopt::Long: 2.5 Hash::Merge: 0.302 JSON: 4.02 LWP::UserAgent: 6.39 Logger::Simple: 2.0 POSIX: 1.76 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.13 Tie::File: 1.02 URI::Escape: 3.31 YAML: 1.31 local::lib: 2.000024 threads: 2.15 threads::shared: 1.56 All 27 Perl modules installed

Checking Environmental Variables... $FUNANNOTATE_DB=/opt/databases $PASAHOME=/venv/opt/pasa-2.4.1 $TRINITYHOME=/venv/opt/trinity-2.8.5 $EVM_HOME=/venv/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config $GENEMARK_PATH=/opt/gmes_linux_64_4 All 6 environmental variables are set

Checking external dependencies... PASA: 2.4.1 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.3.2 bamtools: bamtools 2.5.2 bedtools: bedtools v2.31.1 blat: BLAT v35 diamond: 2.1.8 emapper.py: 2.1.12 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: 36.3.8g glimmerhmm: 3.0.4 gmap: 2017-11-15 hisat2: 2.2.1 hmmscan: HMMER 3.4 (Aug 2023) hmmsearch: HMMER 3.4 (Aug 2023) java: 11.0.8-internal kallisto: 0.46.1 mafft: v7.520 (2023/Mar/22) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.26-r1175 pigz: 2.8 proteinortho: 6.0.16 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.12 snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.9 (July 2021) tantan: tantan 49 tbl2asn: 25.8 tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 ERROR: gmes_petap.pl not installed ERROR: signalp not installed

nextgenusfs commented 3 months ago

Highly unlikely this is going to work in a container. interproscan is a very large tool/database and is not included in the docker image. You would need to have this installed on the same system, again no idea if this will work with container/singulatiry. t

Panda-smile commented 3 months ago

Professoers， the “inpscan” database have been installed correctly。

------------------ 原始邮件 ------------------ 发件人: "nextgenusfs/funannotate" @.>; 发送时间: 2024年3月21日(星期四) 晚上10:54 @.>; @.**@.>; 主题: Re: [nextgenusfs/funannotate] iprscan.xml related erro (Issue #1015)

Highly unlikely this is going to work in a container. interproscan is a very large tool/database and is not included in the docker image. You would need to have this installed on the same system, again no idea if this will work with container/singulatiry. t

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

nextgenusfs / funannotate