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AstrobioMikeAstrobioMike
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update termination message from prodigal problem
1 parent 2d6e907 commit 223b78a

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5 files changed

+39
-10
lines changed

5 files changed

+39
-10
lines changed

‎bin/GToTree‎

Lines changed: 35 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
GREEN='\033[0;32m'
55
RED='\033[0;31m'
66
NC='\033[0m'
7-
VERSION="v1.1.10"
7+
VERSION="v1.1.11"
88

99

1010
if [ "$1" == "--version" ] || [ "$1" == "-v" ]; then
@@ -31,7 +31,7 @@ if [ "$#" == 0 ] || [ $1 == "-h" ] || [ $1 == "help" ]; then
3131
printf " 1) Input genomes in one or any combination of the following formats:\n"
3232
printf " - [-a <file>] single-column file of NCBI assembly accessions\n"
3333
printf " - [-g <file>] single-column file with the paths to each GenBank file\n"
34-
printf " - [-f <file>] single-column file with the paths to each fasta file\n\n"
34+
printf " - [-f <file>] single-column file with the paths to each fasta file\n"
3535
printf " - [-A <file>] single-column file with the paths to each amino acid file,\n"
3636
printf " each file should hold the coding sequences for just one genome\n\n"
3737

@@ -870,7 +870,14 @@ if [ -n "$genbank_list_file" ]; then
870870
printf " Something went wrong with prodigal trying to call genes on the fasta\n" | tee -a $gtotree_log
871871
printf " file generated from assembly ${GREEN}${problem_assembly}${NC}.\n" | tee -a $gtotree_log
872872
printf " GToTree is not sure it should move forward when something odd is going\n" | tee -a $gtotree_log
873-
printf " on like this :(\n" | tee -a $gtotree_log
873+
printf " on like this :(\n\n" | tee -a $gtotree_log
874+
875+
printf " It is possible this is just because this assembly is shorter than\n" | tee -a $gtotree_log
876+
printf " 100,000 bps. That's unlikely to be sufficient for incorporation\n" | tee -a $gtotree_log
877+
printf " into a phylogenomic tree, but if you'd like to still try with it,\n" | tee -a $gtotree_log
878+
printf " you can run prodigal on it yourself and provide the amino acid\n" | tee -a $gtotree_log
879+
printf " sequences to GToTree. Though it is still likely to get filtered\n" | tee -a $gtotree_log
880+
printf " out due to not having enough of the target genes (set with '-G').\n" | tee -a $gtotree_log
874881
printf " ${RED}**************************************************************************** ${NC}\n\n" | tee -a $gtotree_log
875882

876883
printf "\nExiting for now.\n\n" | tee -a $gtotree_log
@@ -904,7 +911,15 @@ if [ -n "$genbank_list_file" ]; then
904911
printf " Something went wrong with prodigal trying to call genes on the fasta\n" | tee -a $gtotree_log
905912
printf " file generated from assembly ${GREEN}${problem_assembly}${NC}.\n" | tee -a $gtotree_log
906913
printf " GToTree is not sure it should move forward when something odd is going\n" | tee -a $gtotree_log
907-
printf " on like this :(\n" | tee -a $gtotree_log
914+
printf " on like this :(\n\n" | tee -a $gtotree_log
915+
916+
917+
printf " It is possible this is just because this assembly is shorter than\n" | tee -a $gtotree_log
918+
printf " 100,000 bps. That's unlikely to be sufficient for incorporation\n" | tee -a $gtotree_log
919+
printf " into a phylogenomic tree, but if you'd like to still try with it,\n" | tee -a $gtotree_log
920+
printf " you can run prodigal on it yourself and provide the amino acid\n" | tee -a $gtotree_log
921+
printf " sequences to GToTree. Though it is still likely to get filtered\n" | tee -a $gtotree_log
922+
printf " out due to not having enough of the target genes (set with '-G').\n" | tee -a $gtotree_log
908923
printf " ${RED}**************************************************************************** ${NC}\n\n" | tee -a $gtotree_log
909924

910925
printf "\nExiting for now.\n\n" | tee -a $gtotree_log
@@ -971,7 +986,14 @@ if [ -n "$fasta_files" ]; then
971986
printf " ${RED}************************** ${NC}REASON FOR TERMINATION ${RED}**************************${NC} \n" | tee -a $gtotree_log
972987
printf " Something went wrong with prodigal trying to call genes on assembly\n" | tee -a $gtotree_log
973988
printf " ${GREEN}${problem_assembly}${NC}. GToTree is not sure it should\n" | tee -a $gtotree_log
974-
printf " move forward when something odd is going on like this :(\n" | tee -a $gtotree_log
989+
printf " move forward when something odd is going on like this :(\n\n" | tee -a $gtotree_log
990+
991+
printf " It is possible this is just because this assembly is shorter than\n" | tee -a $gtotree_log
992+
printf " 100,000 bps. That's unlikely to be sufficient for incorporation\n" | tee -a $gtotree_log
993+
printf " into a phylogenomic tree, but if you'd like to still try with it,\n" | tee -a $gtotree_log
994+
printf " you can run prodigal on it yourself and provide the amino acid\n" | tee -a $gtotree_log
995+
printf " sequences to GToTree. Though it is still likely to get filtered\n" | tee -a $gtotree_log
996+
printf " out due to not having enough of the target genes (set with '-G').\n" | tee -a $gtotree_log
975997
printf " ${RED}**************************************************************************** ${NC}\n\n" | tee -a $gtotree_log
976998

977999
printf "\nExiting for now.\n\n" | tee -a $gtotree_log
@@ -1003,7 +1025,14 @@ if [ -n "$fasta_files" ]; then
10031025
printf " ${RED}************************** ${NC}REASON FOR TERMINATION ${RED}**************************${NC} \n" | tee -a $gtotree_log
10041026
printf " Something went wrong with prodigal trying to call genes on assembly\n" | tee -a $gtotree_log
10051027
printf " ${GREEN}${problem_assembly}${NC}. GToTree is not sure it should\n" | tee -a $gtotree_log
1006-
printf " move forward when something odd is going on like this :(\n" | tee -a $gtotree_log
1028+
printf " move forward when something odd is going on like this :(\n\n" | tee -a $gtotree_log
1029+
1030+
printf " It is possible this is just because this assembly is shorter than\n" | tee -a $gtotree_log
1031+
printf " 100,000 bps. That's unlikely to be sufficient for incorporation\n" | tee -a $gtotree_log
1032+
printf " into a phylogenomic tree, but if you'd like to still try with it,\n" | tee -a $gtotree_log
1033+
printf " you can run prodigal on it yourself and provide the amino acid\n" | tee -a $gtotree_log
1034+
printf " sequences to GToTree. Though it is still likely to get filtered\n" | tee -a $gtotree_log
1035+
printf " out due to not having enough of the target genes (set with '-G').\n" | tee -a $gtotree_log
10071036
printf " ${RED}**************************************************************************** ${NC}\n\n" | tee -a $gtotree_log
10081037

10091038
printf "\nExiting for now.\n\n" | tee -a $gtotree_log

‎bin/gtt-fasta-parallel.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -44,7 +44,7 @@ num=$((num+1)) # to track progress
4444
prodigal -c -q -i $file_location -a ${tmp_dir}/${assembly}_genes1.tmp > /dev/null 2> ${file_location}_prodigal.stderr
4545

4646
if [ -s ${file_location}_prodigal.stderr ]; then
47-
printf "$assembly" >> ${tmp_dir}/kill_fasta_parallel.prodigal
47+
printf "$assembly\n" >> ${tmp_dir}/kill_fasta_parallel.prodigal
4848
rm -rf ${file_location}_prodigal.stderr
4949
exit
5050
else

‎bin/gtt-fasta-serial.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -51,7 +51,7 @@ do
5151
prodigal -c -q -i $file_location -a ${tmp_dir}/${assembly}_genes1.tmp > /dev/null 2> ${file_location}_prodigal.stderr
5252

5353
if [ -s ${file_location}_prodigal.stderr ]; then
54-
printf "$assembly" >> ${tmp_dir}/kill_fasta_serial.prodigal
54+
printf "$assembly\n" >> ${tmp_dir}/kill_fasta_serial.prodigal
5555
rm -rf ${file_location}_prodigal.stderr
5656

5757
exit

‎bin/gtt-genbank-parallel.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -82,7 +82,7 @@ if [ ! -s ${tmp_dir}/${assembly}_genes2.tmp ]; then
8282
prodigal -c -q -i ${tmp_dir}/${assembly}_fasta.tmp -a ${tmp_dir}/${assembly}_genes1.tmp > /dev/null 2> ${file_location}_prodigal.stderr
8383

8484
if [ -s ${file_location}_prodigal.stderr ]; then
85-
printf "$assembly" >> ${tmp_dir}/kill_genbank_parallel.prodigal
85+
printf "$assembly\n" >> ${tmp_dir}/kill_genbank_parallel.prodigal
8686
rm -rf ${file_location}_prodigal.stderr
8787
exit
8888
else

‎bin/gtt-genbank-serial.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -86,7 +86,7 @@ do
8686
prodigal -c -q -i ${tmp_dir}/${assembly}_fasta.tmp -a ${tmp_dir}/${assembly}_genes1.tmp > /dev/null 2> ${file_location}_prodigal.stderr
8787

8888
if [ -s ${file_location}_prodigal.stderr ]; then
89-
printf "$assembly" >> ${tmp_dir}/kill_genbank_serial.prodigal
89+
printf "$assembly\n" >> ${tmp_dir}/kill_genbank_serial.prodigal
9090
rm -rf ${file_location}_prodigal.stderr
9191
exit
9292
else

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