nextgenusfs
funannotate mask error
When we use "funannotate mask" to Mask repetitive sequences, an error message appeared [，what's puzzling is that currently this error only appears in the genome of Flammulina velutipes and other species are operating normally.
Running record
(funannotate) [liuyuanchao@master01 /data/liuyuanchao/funannotate_test/Analysis/Flammulina_velutipes] $ls -l total 37712 -rwxr-xr-x 1 liuyuanchao liuyuanchao 38605067 Nov 25 15:57 GCA_011800155.1_ASM1180015v1_genomic.fna -rwxr-xr-x 1 liuyuanchao liuyuanchao 470 Nov 25 15:53 LongSequence_ID_Rename.pl -rwxr-xr-x 1 liuyuanchao liuyuanchao 865 Nov 25 15:54 work.sh (funannotate) [liuyuanchao@master01 /data/liuyuanchao/funannotate_test/Analysis/Flammulina_velutipes] $funannotate mask -i GCA_011800155.1_ASM1180015v1_genomic.fna --cpus 48 -o ./GCA_011800155.1_ASM1180015v1_genomic.fna
[Nov 25 03:59 PM]: OS: CentOS Linux 7, 160 cores, ~ 958 GB RAM. Python: 3.9.7
[Nov 25 03:59 PM]: Running funanotate v1.8.7
[Nov 25 03:59 PM]: Soft-masking simple repeats with tantan
Traceback (most recent call last):
File "/opt/anaconda3/envs/funannotate/bin/funannotate", line 10, in
$funannotate check --show-versions
Checking dependencies for 1.8.7
You are running Python v 3.9.7. Now checking python packages... biopython: 1.79 goatools: 1.1.6 matplotlib: 3.4.3 natsort: 8.0.0 numpy: 1.21.4 pandas: 1.3.4 psutil: 5.8.0 requests: 2.26.0 scikit-learn: 1.0.1 scipy: 1.7.0 seaborn: 0.11.2 All 11 python packages installed
You are running Perl v b'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: 1.855 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=/data/liuyuanchao/funannotate_test/all_database $PASAHOME=/opt/anaconda3/envs/funannotate/opt/pasa-2.4.1 $TRINITY_HOME=/opt/anaconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/opt/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/opt/anaconda3/envs/funannotate/config/ ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir
Checking external dependencies... PASA: 2.4.1 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.3.3 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v36 diamond: 2.0.8 emapper.py: 2.1.3 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2018-07-04 gmes_petap.pl: 4.68_lic hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 11.0.8-internal kallisto: 0.46.1 mafft: v7.490 (2021/Oct/30) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.22-r1101 proteinortho: 6.0.31 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.10 signalp: 5.0b snap: 2006-07-28 stringtie: 2.1.7 tRNAscan-SE: 2.0.9 (July 2021) tantan: tantan 26 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 36 external dependencies are installed
