nextgenusfs
commented
1 year ago Hi @kate-stankiewicz, I've not seen this one yet. I found the same thing you did it seems: https://stackoverflow.com/questions/72103046/libtinfo-so-6-no-version-information-available-message-using-conda-environment. As far as I know you should just need a working version of samtools in your PATH, ie it doesn't need to be from conda, so you could remove the conda version and add one from somewhere else. Not sure what else to try. Otherwise sometimes trying to re-create the conda environment from scratch could help. There should be a new version on conda as of this morning.
kate-stankiewicz
Hello,
First thanks for this great tool! I have used funannotate in the past and it's very useful. I recently installed it on a new machine and have been encountering issues.
When running:
funannotate test -t all --cpus 2
It fails at the trinity step:
[Apr 04 05:48 PM]: CMD ERROR: Trinity --no_distributed_trinity_exec --genome_guided_bam rna-seq/update_misc/hisat2.coordSorted.bam --genome_guided_max_intron 3000 --CPU 2 --max_memory 50G --output rna-seq/update_misc/trinity_gg [Apr 04 05:48 PM]: ERROR: Trinity de novo assembly failed
I inspected the Trinity logfile (found here: rna-seq/update_misc/Trinity-gg.log ) and I see this:
Trinity version: Trinity-v2.8.5 Tuesday, April 4, 2023: 17:48:11 CMD: /users/kstankie/anaconda3/envs/funannotate/opt/trinity-2.8.5/util/support_scripts/ensure_coord_sorted_sam.pl rna-seq/update_misc/hisat2.coordSorted.bam ** NOTE: Latest version of Trinity is Trinity-v2.15.1, and can be obtained at: https://github.com/trinityrnaseq/trinityrnaseq/releases
samtools: /users/kstankie/anaconda3/envs/funannotate/bin/../lib/libtinfow.so.6: no version information available (required by samtools) samtools: /users/kstankie/anaconda3/envs/funannotate/bin/../lib/libncursesw.so.6: no version information available (required by samtools) samtools: /users/kstankie/anaconda3/envs/funannotate/bin/../lib/libncursesw.so.6: no version information available (required by samtools) -appears to be a coordinate sorted bam file. ok. Argument "/users/kstankie/anaconda3/envs/funannotate/bin/" isn't numeric in numeric ne (!=) at /users/kstankie/anaconda3/envs/funannotate/bin/Trinity line 3812. Error, need samtools installed that is at least as new as version 1.3 at /users/kstankie/anaconda3/envs/funannotate/bin/Trinity line 3813.
The output of "funannotate check --show-versions" shows these same libtinfow.so.6 type issues for samtools:
Checking dependencies for 1.8.13
You are running Python v 3.8.16. Now checking python packages... biopython: 1.77 goatools: 1.2.3 matplotlib: 3.4.3 natsort: 8.3.1 numpy: 1.24.2 pandas: 1.5.3 psutil: 5.9.4 requests: 2.28.2 scikit-learn: 1.2.2 scipy: 1.10.1 seaborn: 0.12.2 All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.50 Clone: 0.46 DBD::SQLite: 1.72 DBD::mysql: 4.050 DBI: 1.643 DB_File: 1.855 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: 5.12 YAML: 1.30 threads: 2.25 threads::shared: 1.61 ERROR: local::lib not installed, install with cpanm local::lib
Checking Environmental Variables... $FUNANNOTATE_DB=/users/kstankie/funannotate_db $PASAHOME=/users/kstankie/anaconda3/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/users/kstankie/anaconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/users/kstankie/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/users/kstankie/anaconda3/envs/funannotate/config/ $GENEMARK_PATH=/proj/omics4tb2/kstankiewicz/work/geneMark/gmes_linux_64_4 All 6 environmental variables are set
Checking external dependencies... samtools: /users/kstankie/anaconda3/envs/funannotate/bin/../lib/libtinfow.so.6: no version information available (required by samtools) samtools: /users/kstankie/anaconda3/envs/funannotate/bin/../lib/libncursesw.so.6: no version information available (required by samtools) samtools: /users/kstankie/anaconda3/envs/funannotate/bin/../lib/libncursesw.so.6: no version information available (required by samtools) PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.4.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.1.6 emapper.py: There was an error retrieving eggnog-mapper DB data: not a valid file "/users/kstankie/anaconda3/envs/funannotate/lib/python3.8/site-packages/data/eggnog.db" Maybe you need to run download_eggnog_data.py emapper-2.1.10 / Expected eggNOG DB version: 5.0.2 / Installed eggNOG DB version: unknown / Diamond found: diamond 2.1.6 / MMseqs2 found: 14.7e284
ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2021-08-25 gmes_petap.pl: 4.71_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: v7.520 (2023/Mar/22) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: pigz 2.6 proteinortho: 6.2.2 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.16.1 signalp: 4.1 snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.11 (Oct 2022) tantan: tantan 40 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 All 37 external dependencies are installed
I have tried to fix this by installing the ncurses package specifically from conda-forge:
packages in environment at /users/kstankie/anaconda3/envs/funannotate:
#
Name Version Build Channel
ncurses 6.3 h9c3ff4c_0 conda-forge
However, this did not solve the issue. I also have tried a few different versions of samtools, which has also not solved the problem. I didn't see this particular issue posted here before, so am wondering if anyone has any idea on how to solve it?
Many thanks!