Not sucessful when install funannotate with Conda on HPC

[chenpingau]

Are you using the latest release?
Yes

Describe the bug
I tried to install funannotate on HPC
I followed the instructions EXACTLY from https://funannotate.readthedocs.io/en/latest/install.html
But still not successful.

There are several errors (refer to the below output of "funannotate check --show-versions")

1. ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir

2. samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

3. fasta: no way to determine

4. pslCDnaFilter: no way to determine

5. tbl2asn: no way to determine, likely 25.X

6.     ERROR: emapper.py not installed
    ERROR: ete3 not installed
    ERROR: gmes_petap.pl not installed
    ERROR: samtools not installed
    ERROR: signalp not installed
   

I have some experience with HPC, a little experiences with Conda, and totally new with funannotate. I have no idea how to fix the above issues.

Could anyone help me with above issues?

What command did you issue?

then create environment

$ conda create --name funannotate01 python=2.7 funannotate

start up conda ENV

$ conda activate funannotate01

check that all modules are installed

$ funannotate check --show-versions

download/setup databases to a writable/readable location

$ funannotate setup -d /home/chenpingau/tools/funannotate_db_01

set ENV variable for $FUNANNOTATE_DB

echo "export FUNANNOTATE_DB=/home/chenpingau/tools/funannotate_db_01" > /home/chenpingau/.conda/envs/funannotate01/etc/conda/activate.d/funannotate.sh
echo "unset FUNANNOTATE_DB" > /home/chenpingau/.conda/envs/funannotate01/etc/conda/deactivate.d/funannotate.sh

Logfiles
Please provide relavent log files of the error.

OS/Install Information
(base)
/home/chenpingau/tools
$ conda activate funannotate01
(funannotate01)
/home/chenpingau/tools
$ funannotate check --show-versions

Checking dependencies for 1.7.4

You are running Python v 2.7.15. Now checking python packages...
biopython: 1.76
goatools: 0.6.4
matplotlib: 2.2.4
natsort: 6.2.0
numpy: 1.16.5
pandas: 0.24.2
psutil: 5.7.0
requests: 2.23.0
scikit-learn: 0.20.3
scipy: 1.2.1
seaborn: 0.9.0
All 11 python packages installed

You are running Perl v 5.026002. Now checking perl modules...
Bio::Perl: 1.007002
Carp: 1.38
Clone: 0.42
DBD::SQLite: 1.64
DBD::mysql: 4.046
DBI: 1.642
DB_File: 1.852
Data::Dumper: 2.173
File::Basename: 2.85
File::Which: 1.23
Getopt::Long: 2.5
Hash::Merge: 0.300
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: 3.12
Tie::File: 1.02
URI::Escape: 3.31
YAML: 1.29
threads: 2.15
threads::shared: 1.56
All 27 Perl modules installed

Checking Environmental Variables...
$FUNANNOTATE_DB=/home/chenpingau/tools/funannotate_db_01
$PASAHOME=/home/chenpingau/.conda/envs/funannotate01/opt/pasa-2.4.1
$TRINITY_HOME=/home/chenpingau/.conda/envs/funannotate01/opt/trinity-2.8.5
$EVM_HOME=/home/chenpingau/.conda/envs/funannotate01/opt/evidencemodeler-1.1.1
$AUGUSTUS_CONFIG_PATH=/home/chenpingau/.conda/envs/funannotate01/config/
ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir

Checking external dependencies...
samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
PASA: 2.4.1
CodingQuarry: 2.0
Trinity: 2.8.5
augustus: 3.3.2
bamtools: bamtools 2.5.1
bedtools: bedtools v2.29.2
blat: BLAT v36
diamond: 0.9.24
exonerate: exonerate 2.4.0
fasta: no way to determine
glimmerhmm: 3.0.4
gmap: 2017-11-15
hisat2: 2.2.0
hmmscan: HMMER 3.3 (Nov 2019)
hmmsearch: HMMER 3.3 (Nov 2019)
java: 11.0.1
kallisto: 0.46.2
mafft: v7.464 (2020/Apr/21)
makeblastdb: makeblastdb 2.2.31+
minimap2: 2.17-r941
proteinortho: 6.0.16
pslCDnaFilter: no way to determine
salmon: salmon 0.14.1
snap: 2006-07-28
stringtie: 2.1.2
tRNAscan-SE: 2.0.5 (October 2019)
tantan: tantan 13
tbl2asn: no way to determine, likely 25.X
tblastn: tblastn 2.2.31+
trimal: trimAl v1.4.rev15 build[2013-12-17]
trimmomatic: 0.39
ERROR: emapper.py not installed
ERROR: ete3 not installed
ERROR: gmes_petap.pl not installed
ERROR: samtools not installed
ERROR: signalp not installed
(funannotate01)
/home/chenpingau/tools

[nextgenusfs]

See here for some tips #389. You have to install GeneMark manually due to licensing. The other errors are not errors, just telling you there is no way to determine version in that particular software. Try a different version of samtools on bioconda, this is a common problem with some dependencies.

I suspect that you have packages installed in your base conda directory, hence some dependencies get adjusted by conda.

[chenpingau]

@nextgenusfs, thank you for your quick reply!

I found on HPC it has GeneMark-ES module.

Now I ran

$ module load genemark-es/4.33

before starting the Conda environment. Then I ran the following test:

$ funannotate test -t all --cpus 1

I already found the famous GeneMark license issue happened in the test

I'll try to solve this license issue and other issues if there any.

Thank you again!