sat-assembler exits with no output and no error message

[Jonathan Young]

Hi,

I'm having trouble getting SAT-assembler.sh to run correctly, the script runs until the the translated sequence files are built (I can see them in the output folder while the script is running) but after this stage completes the script exits with no error message and the translated sequence files are deleted leaving an empty output folder

I've tried running the script as described in your paper using the same dataset and HMM profile and get the same problem

when debugging the script using sudo bash -x i get the following output (this was from a run I attempted using a 16s HMM profile which works well with this dataset when used with hmmsearch):

*****Start of output*******

lab-0g414@lab0g414:/media/Jonathan/sat_assembler/SAT-Assembler$ sudo bash -x ./SAT-Assembler.sh -m /media/Jonathan/final_tax/bbduk/rRNASelector_for_linux/lib/16s_bact_rev3.hmm -f /media/Jonathan/tageted_gene_assembly/combinedv10c.fna -o 16s_test
[sudo] password for lab-0g414:
+ hmm=
+ fasta=
+ t=20
+ d=0.15
+ out=
+++ dirname ./SAT-Assembler.sh
++ cd .
++ pwd
+ DIR=/media/Jonathan/sat_assembler/SAT-Assembler
+ getopts hm:f:t:d:o: OPTION
+ case $OPTION in
+ hmm=/media/Jonathan/final_tax/bbduk/rRNASelector_for_linux/lib/16s_bact_rev3.hmm
+ getopts hm:f:t:d:o: OPTION
+ case $OPTION in
+ fasta=/media/Jonathan/tageted_gene_assembly/combinedv10c.fna
+ getopts hm:f:t:d:o: OPTION
+ case $OPTION in
+ out=16s_test
+ getopts hm:f:t:d:o: OPTION
+ '[' /media/Jonathan/final_tax/bbduk/rRNASelector_for_linux/lib/16s_bact_rev3.hmm == '' ']'
+ '[' /media/Jonathan/tageted_gene_assembly/combinedv10c.fna == '' ']'
+ '[' 16s_test == '' ']'
++ which hmmsearch
++ wc -l
+ '[' 1 -eq 0 ']'
++ /media/Jonathan/sat_assembler/SAT-Assembler/check_python_packages.py
+ '[' 0 -eq 1 ']'
+ '[' '!' -d 16s_test/ ']'
+ mkdir 16s_test/
++ cd 16s_test
++ pwd
+ tmp=/media/Jonathan/sat_assembler/SAT-Assembler/16s_test
++ echo /media/Jonathan/tageted_gene_assembly/combinedv10c.fna
++ awk '{split($1,a,"/"); print a[length(a)]}'
+ base_fasta=combinedv10c.fna
+ /media/Jonathan/sat_assembler/SAT-Assembler/DNA2Protein 1-6 /media/Jonathan/tageted_gene_assembly/combinedv10c.fna /media/Jonathan/sat_assembler/SAT-Assembler/16s_test/combinedv10c.fna
+ python /media/Jonathan/sat_assembler/SAT-Assembler/parse_hmm_files.py /media/Jonathan/final_tax/bbduk/rRNASelector_for_linux/lib/16s_bact_rev3.hmm /media/Jonathan/sat_assembler/SAT-Assembler/16s_test/HMMs
+ ls /media/Jonathan/sat_assembler/SAT-Assembler/16s_test/HMMs
+ read line
+ rm -r /media/Jonathan/sat_assembler/SAT-Assembler/16s_test/HMMs
+ rm /media/Jonathan/sat_assembler/SAT-Assembler/16s_test/combinedv10c.fna.frame1 /media/Jonathan/sat_assembler/SAT-Assembler/16s_test/combinedv10c.fna.frame2 /media/Jonathan/sat_assembler/SAT-Assembler/16s_test/combinedv10c.fna.frame3 /media/Jonathan/sat_assembler/SAT-Assembler/16s_test/combinedv10c.fna.frame4 /media/Jonathan/sat_assembler/SAT-Assembler/16s_test/combinedv10c.fna.frame5 /media/Jonathan/sat_assembler/SAT-Assembler/16s_test/combinedv10c.fna.frame6
****end of output*******

I've double and triple checked that I have all the dependancies installed which are listed in the documentation. I can't for the life of me figure out why the script wont run

any help at all would be greatly appreciated,

Thanks,

Jonny