Hi all,
I'm a bit of a novice when it comes to programming with only basic training so this problem seems to be a little over my head.
So I know this issue has been addressed before with run_lips4.pl but the resulting solutions for that seem to be either an improper name creation or a blank blast file due to incorrect blast database downloads. While my error seems to be specific to alignblast.pl.
I run run_lips4.pl with the following command:
./run_lips.pl ./caveolin3.fasta ./caveolin3.span blastpgp $BLASTDB/nr ./alignblast.pl -v 4
Here is where I am. I had issues with the nr database and other things but evertually I figured it out and created what appears to be a ligitament file.blast file. It has ~75000 lines in it.
using a series of print commands I've isolated the problem to this loop.
# Search for "Results from round"
# If found, we are looking at PsiBlast output and have to search for the beginning of the last round
$line_number++;
print "line_number = $line_number\n"; #my inserted print command to see what $line_number is.
for ($i=1; $i<=9; $i++)
{
$line=<INFILE>;
print "line = $line \n"; #my inserted print command to let me what $line is.
if (!$line) {die("Error in alignblast.pl: blast output file $infile truncated:$!\n");}
$line_number++;
if ($line=~/^Results from round/)
{
# PsiBlast output! Search for line number with last occurence of "Results from round"
if ($v>=3) {print("PsiBlast output with several rounds detected. Searching for last round...\n");}
and here is the last few line on my output:
line_number = 74886
line = Gap Penalties: Existence: 11, Extension: 1
line = Neighboring words threshold: 11
line_number = 74887
line = Neighboring words threshold: 11
line = Window for multiple hits: 40
line_number = 74888
line = Window for multiple hits: 40
E-value maximum : 0.001
coverage threshold : 0
sequence id threshold : 0
score/column threshold : -10
Blast file : caveolin3.blast
Output file : caveolin3.blast.msa
Output format : psi
Query length = 0
Use of uninitialized value $j in concatenation (.) or string at ./alignblast.pl line 209, <INFILE> line 0.000000.
Use of uninitialized value $j in array element at ./alignblast.pl line 209, <INFILE> line 0.000000.
Use of uninitialized value in concatenation (.) or string at ./alignblast.pl line 209, <INFILE> line 0.000000.
j = queryseqj = line_number = 74888
line_number = 74889
Use of uninitialized value $line in concatenation (.) or string at ./alignblast.pl line 217, <INFILE> line 0.000000.
line =
Error in alignblast.pl: blast output file caveolin3.blast truncated:
It appears that instead of starting from the FIRST line of the LAST result it just starts from the last line adds one to make it 74889 then fails. In addition some cariables are uninitialized even though they are initialized early on. you can see this with the variable $line which has values until it gets into the for loop then becomes unitialized (maybe because the value is End Of File and an invalid value?).
This output is my output when I just run the alignblast.pl script with the line from run_lips4.pl as follows
./alignblast.pl caveolin3.blast caveolin3.blast.msa -psi
I've attached my alignblast.pl script with the added print lines for debugging. I attempted to attach a full output with the print lines and a full blast file but they are too large so but you can get an idea of the format for the last few lines from the print $line output above.
Thanks for any help you can give and if there is any suggestions for how to attach large files please let me know,
Ryan
I've changed to file endings to .txt for uploading purposes