JAMg complained that some files and directories cannot be found

[yjx1217]

I suspect that this is due to incorrect path or file name information coded in JAMg. I highlighted those error messages. See the log file below:

~/Analysis/S288c_pilon_JAMg/exon_search ~/Analysis/S288c_pilon_JAMg
Use of uninitialized value $repeatmasker_options in concatenation (.) or string at /home/yjx/Programs/JAMg/bin/prepare_domain_exon_annotation.pl line 936.
Use of uninitialized value $repeatmasker_options in concatenation (.) or string at /home/yjx/Programs/JAMg/bin/prepare_domain_exon_annotation.pl line 937.
Masking repeats with 4 CPUs (cf /home/yjx/Analysis/S288c_pilon_JAMg/S288c_pilon.fasta.repeatmasking.log)..
Repeat options:
CMD: /home/yjx/Programs/RepeatMasker/RepeatMasker -e ncbi -frag 5000000 -gff -pa 4 -qq /home/yjx/Analysis/S288c_pilon_JAMg/S288c_pilon.fasta 2>&1 > /home/yj
RepeatMasking completed and hints file produced (/home/yjx/Analysis/S288c_pilon_JAMg/S288c_pilon.fasta.out.gff)
CMD: /usr/local/bin/getorf -sequence /home/yjx/Analysis/S288c_pilon_JAMg/S288c_pilon.fasta.masked -outseq /home/yjx/Analysis/S288c_pilon_JAMg/S288c_pilon.fas
Find and extract open reading frames (ORFs)
CMD: /usr/local/bin/getorf -sequence /home/yjx/Analysis/S288c_pilon_JAMg/S288c_pilon.fasta.masked -outseq /home/yjx/Analysis/S288c_pilon_JAMg/S288c_pilon.fas
Find and extract open reading frames (ORFs)
Post-processing...
/home/yjx/Analysis/S288c_pilon_JAMg/S288c_pilon.fasta.masked.exons.aa: Found 13097 exons and 12213 passing criteria
Preparing HHblits files for local
CMD: /home/yjx/Programs/JAMg/3rd_party/hhsuite/bin/ffindex_from_fasta -s /home/yjx/Analysis/S288c_pilon_JAMg/S288c_pilon.fasta.masked.exons.aa.trim.db /home/
Processing transposon library
Processing with 10 CPUs...
^M 1 / 12213 ^M 2 / 12213 ^M 3 / 12213 ^M 4 / 12213 ^M 5 / 12213 ^M 6 / 12213
cat: /home/yjx/Analysis/S288c_pilon_JAMg/S288c_pilon.fasta.masked.exons.aa.trim.transposons.hhr_.idx_: No such file or directory
CMD: cat /home/yjx/Analysis/S288c_pilon_JAMg/S288c_pilon.fasta.masked.exons.aa.trim.transposons.hhr* | tr -d '\000' > /home/yjx/Analysis/S288c_pilon_JAMg/hhr
Post-processing /home/yjx/Analysis/S288c_pilon_JAMg/hhr.S288c_pilon.fasta.masked.exons.aa.trim.transposons.hhr
CMD: /home/yjx/Programs/JAMg/3rd_party/hhsuite/bin/ffindex_from_fasta -s /home/yjx/Analysis/S288c_pilon_JAMg/S288c_pilon.fasta.masked.exons.aa.trim.norep.db
Processing UniProt library
Processing with 10 CPUs...
^M 1 / 11756 ^M 2 / 11756 ^M 3 / 11756 ^M 4 / 11756 ^M 5 / 11756 ^M 6 / 11756
cat: /home/yjx/Analysis/S288c_pilon_JAMg/S288c_pilon.fasta.masked.exons.aa.trim.norep.uniprot.hhr_.idx_: No such file or directory
CMD: cat /home/yjx/Analysis/S288c_pilon_JAMg/S288c_pilon.fasta.masked.exons.aa.trim.norep.uniprot.hhr* | tr -d '\000' > /home/yjx/Analysis/S288c_pilon_JAMg/h
Post-processing /home/yjx/Analysis/S288c_pilon_JAMg/hhr.S288c_pilon.fasta.masked.exons.aa.trim.norep.uniprot.hhr
ls: cannot access ./_hints: No such file or directory
ln: accessing exon_search/_masked': No such file or directory ln: accessing exon_search/*.out.gff': No such file or directory