Open YDD99 opened 1 year ago
hyphaltip
commented
1 year ago can you do a git clone and then pip? it sounds like from errors your git clone is failing - is there any issues with your network connection or internet proxies?
git clone https://github.com/nextgenusfs/funannotate.git
cd funannotate
pip install .
YDD99
commented
1 year ago than you for your help,after i did this, the new problem come out
You are running Python v 3.7.12. Now checking python packages... biopython: 1.79 goatools: 1.2.3 matplotlib: 3.5.3 natsort: 8.2.0 numpy: 1.21.6 pandas: 1.3.5 psutil: 5.9.2 requests: 2.28.1 scikit-learn: 1.0.2 scipy: 1.7.3 seaborn: 0.12.0 All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.38 Clone: 0.42 DBD::SQLite: 1.70 DBD::mysql: 4.046 DBI: 1.643 DB_File: 1.855 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.52 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: 5.12 YAML: 1.30 local::lib: 2.000029 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed
Checking external dependencies... ERROR: pslDnaFiler found but error running: pslCDnaFilter: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory
You are running Python v 3.7.12. Now checking python packages... biopython: 1.79 goatools: 1.2.3 matplotlib: 3.5.3 natsort: 8.2.0 numpy: 1.21.6 pandas: 1.3.5 psutil: 5.9.2 requests: 2.28.1 scikit-learn: 1.0.2 scipy: 1.7.3 seaborn: 0.12.0 All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.38 Clone: 0.42 DBD::SQLite: 1.70 DBD::mysql: 4.046 DBI: 1.643 DB_File: 1.855 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.52 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: 5.12 YAML: 1.30 local::lib: 2.000029 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed
Checking external dependencies... ERROR: pslDnaFiler found but error running: pslCDnaFilter: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory
PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.5.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.0.15 emapper.py: 2.1.9 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: 36.3.8g glimmerhmm: 3.0.4 gmap: 2021-08-25 gmes_petap.pl: 4.69_lic 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: v7.508 (2022/Sep/07) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: 2.6 proteinortho: 6.1.1 salmon: salmon 0.14.1 samtools: samtools 1.16.1 signalp: 5.0b snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.11 (Oct 2022) tantan: tantan 39 tbl2asn: 25.8 tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.36 ERROR: pslCDnaFilter not installed
then i use conda install ucsc-pslcdnafilter and check ,but no help
i also use wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslCDnaFilter and also not work, thankyou
YDD99
commented
1 year ago than you for your help,after i did this, the new problem come out
(funannotate) @.***:~$ funannotate check --show-versions
Checking dependencies for 1.8.14
You are running Python v 3.7.12. Now checking python packages... biopython: 1.79 goatools: 1.2.3 matplotlib: 3.5.3 natsort: 8.2.0 numpy: 1.21.6 pandas: 1.3.5 psutil: 5.9.2 requests: 2.28.1 scikit-learn: 1.0.2 scipy: 1.7.3 seaborn: 0.12.0 All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.38 Clone: 0.42 DBD::SQLite: 1.70 DBD::mysql: 4.046 DBI: 1.643 DB_File: 1.855 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.52 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: 5.12 YAML: 1.30 local::lib: 2.000029 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed
Checking Environmental Variables... $FUNANNOTATE_DB=/home/wangyuanbing/funannotate_db $PASAHOME=/home/wangyuanbing/miniconda3/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/home/wangyuanbing/miniconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/home/wangyuanbing/miniconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/home/wangyuanbing/miniconda3/envs/funannotate/config/ $GENEMARK_PATH=/home/wangyuanbing/miniconda3/envs/funannotate/bin:/home/wangyuanbing/miniconda3/bin:/home/wangyuanbing/miniconda3/condabin:/home/wangyuanbing/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin All 6 environmental variables are set
Checking external dependencies... ERROR: pslDnaFiler found but error running: pslCDnaFilter: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory
PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.5.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.0.15 emapper.py: 2.1.9 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: 36.3.8g glimmerhmm: 3.0.4 gmap: 2021-08-25 gmes_petap.pl: 4.69_lic hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 17.0.3-internal kallisto: 0.46.1 mafft: v7.508 (2022/Sep/07) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: 2.6 proteinortho: 6.1.1 salmon: salmon 0.14.1 samtools: samtools 1.16.1 signalp: 5.0b snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.11 (Oct 2022) tantan: tantan 39 tbl2asn: 25.8 tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.36 ERROR: pslCDnaFilter not installed (funannotate) @.***:~$ funannotate check --show-versions
Checking dependencies for 1.8.14
You are running Python v 3.7.12. Now checking python packages... biopython: 1.79 goatools: 1.2.3 matplotlib: 3.5.3 natsort: 8.2.0 numpy: 1.21.6 pandas: 1.3.5 psutil: 5.9.2 requests: 2.28.1 scikit-learn: 1.0.2 scipy: 1.7.3 seaborn: 0.12.0 All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.38 Clone: 0.42 DBD::SQLite: 1.70 DBD::mysql: 4.046 DBI: 1.643 DB_File: 1.855 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.52 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: 5.12 YAML: 1.30 local::lib: 2.000029 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed
Checking Environmental Variables... $FUNANNOTATE_DB=/home/wangyuanbing/funannotate_db $PASAHOME=/home/wangyuanbing/miniconda3/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/home/wangyuanbing/miniconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/home/wangyuanbing/miniconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/home/wangyuanbing/miniconda3/envs/funannotate/config/ $GENEMARK_PATH=/home/wangyuanbing/miniconda3/envs/funannotate/bin:/home/wangyuanbing/miniconda3/bin:/home/wangyuanbing/miniconda3/condabin:/home/wangyuanbing/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin All 6 environmental variables are set
Checking external dependencies... ERROR: pslDnaFiler found but error running: pslCDnaFilter: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory
PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.5.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.0.15 emapper.py: 2.1.9 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: 36.3.8g glimmerhmm: 3.0.4 gmap: 2021-08-25 gmes_petap.pl: 4.69_lic 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: v7.508 (2022/Sep/07) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: 2.6 proteinortho: 6.1.1 salmon: salmon 0.14.1 samtools: samtools 1.16.1 signalp: 5.0b snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.11 (Oct 2022) tantan: tantan 39 tbl2asn: 25.8 tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.36 ERROR: pslCDnaFilter not installed
then i use conda install ucsc-pslcdnafilter and check ,but no help i also use wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslCDnaFilter and also not work, thank you
Checking external dependencies... ERROR: pslDnaFiler found but error running: pslCDnaFilter: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory
ERROR: pslCDnaFilter not installed
------------------ 原始邮件 ------------------ 发件人: "nextgenusfs/funannotate" @.>; 发送时间: 2022年11月15日(星期二) 晚上8:58 @.>; @.**@.>; 主题: Re: [nextgenusfs/funannotate] can't updated (Issue #839)
can you do a git clone and then pip? it sounds like from errors your git clone is failing - is there any issues with your network connection or internet proxies?
git clone https://github.com/nextgenusfs/funannotate.git cd funannotate pip install .
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Reply to this email directly, view it on GitHub, or unsubscribe.
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hyphaltip
commented
1 year ago the missing pslCDnaFilter should not holding up your update - your error message above was about installing funannotate? Can you re-state the problem you are trying to solve that is not working?
YDD99
commented
1 year ago thank you , the updated was successful, but funannotate check --version display
To print all dependencies and versions: funannotate check --show-versions
You are running Python v 3.7.12. Now checking python packages... All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules... All 27 Perl modules installed
Checking external dependencies... ERROR: pslDnaFiler found but error running: pslCDnaFilter: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory
ERROR: pslCDnaFilter not installedi try to use conda install ucsc-pslcdnafilter or wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/pslCDnaFilter and it didn't work, so what should i do about pslCDnaFilter
(funannotate) wangyuanbing@wangyb-System:~/Desktop/CZY/funannotate$ python -m pip install git+https://github.com/nextgenusfs/funannotate.git Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple Collecting git+https://github.com/nextgenusfs/funannotate.git Cloning https://github.com/nextgenusfs/funannotate.git to /tmp/pip-req-build-9dl0b7l3 Running command git clone --filter=blob:none --quiet https://github.com/nextgenusfs/funannotate.git /tmp/pip-req-build-9dl0b7l3
fatal: unable to access 'https://github.com/nextgenusfs/funannotate.git/': GnuTLS recv error (-110): The TLS connection was non-properly terminated. warning: Clone succeeded, but checkout failed. You can inspect what was checked out with 'git status' and retry with 'git restore --source=HEAD :/'
error: subprocess-exited-with-error
× git clone --filter=blob:none --quiet https://github.com/nextgenusfs/funannotate.git /tmp/pip-req-build-9dl0b7l3 did not run successfully. │ exit code: 128 ╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error
× git clone --filter=blob:none --quiet https://github.com/nextgenusfs/funannotate.git /tmp/pip-req-build-9dl0b7l3 did not run successfully. │ exit code: 128 ╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip. (funannotate) wangyuanbing@wangyb-System:~/Desktop/CZY/funannotate$ (funannotate) wangyuanbing@wangyb-System:~/Desktop/CZY/funannotate$ (funannotate) wangyuanbing@wangyb-System:~/Desktop/CZY/funannotate$