Iqdd Problem - Detecting Microsatellites From Whole Genome Data

Question

[Alex Twyford]

I am trying to use iQDD to locate microsatellites from a whole plant genome. Whenever I try and use the programme I get the same error message:

Cannot access to folder datatemp1

I am to my knowledge following the instructions to the letter, so I have no idea what is wrong! Any help is appreciated. I have tried it with my own data and the example data with teh same problem. Below is the full details.

Best wishes, Alex

perl sort_length.pl win c:\QDD_tetetemp\sample_test c:\QDD_tetetemp\sample_test 80 \.fas
perl find_and_mask_ms.pl 10000000 4 4 4 4 4 1 0 c:\QDD_tetetemp\sample_test c:\QDD_tetetemp\sample_test bp\.fas
1 file(s) copied.
1 File(s) copied
1 File(s) copied
>>>>>>>>>>>>>> Searching motifs step done. <<<<<<<<<<<<<<<<<
del_files = 1
blast_path = C:\Program Files\iQDD
folder = C:\Program Files\iQDD\data 2
length_limit = 80
min1 = 10000000
min2 = 4
min3 = 4
min4 = 4
min5 = 4
min6 = 4
e_tag = 1E-1
word_size = 7
Evector = 1E-3
tag = 0
adapter = 0
system = win
1 file(s) copied.
********** sample_test.fas **********
1 file(s) copied.
perl sort_length.pl win c:\QDD_tetetemp\sample_test c:\QDD_tetetemp\sample_test 80 \.fas
perl find_and_mask_ms.pl 10000000 4 4 4 4 4 1 0 c:\QDD_tetetemp\sample_test c:\QDD_tetetemp\sample_test bp\.fas
1 file(s) copied.
1 File(s) copied
1 File(s) copied
>>>>>>>>>>>>>> Searching motifs step done. <<<<<<<<<<<<<<<<<
del_files = 1
blast_path = C:\Program Files\iQDD
clust_path = C:\Program Files\ClustalW2\
clust_ver = 2
gr_limit = 0.05
min1 = 8
min2 = 4
min3 = 4
min4 = 4
min5 = 4
min6 = 4
E_blast = 1E-40
system = win
folder = C:\Program Files\iQDD\data 2
prop_maj = 0.66
cons_calc = 1
1 file(s) copied.
********** sample_test_pipe2.fas **********
1 file(s) copied.
perl find_and_mask_ms.pl 8 4 4 4 4 4 1 0 c:\QDD_tetetemp\sample_test_pipe2 c:\QDD_tetetemp\sample_test_pipe2 pipe2\.fas
perl group_seq_var2.pl 1E-40 "C:\Program Files\iQDD\" win c:\QDD_tetetemp\sample_test_pipe2 c:\QDD_tetetemp\sample_test_pipe2 _mask\.fas
Cannot access to folder datatemp1
perl find_and_mask_ms.pl 8 4 4 4 4 4 1 0 c:\QDD_tetetemp\sample_test_pipe2 c:\QDD_tetetemp\sample_test_pipe2 _nr\.fas
perl calc_ident2.pl win c:\QDD_tetetemp\sample_test_pipe2 c:\QDD_tetetemp\sample_test_pipe2 "C:\Program Files\iQDD\" "C:\Program Files\ClustalW2\\" 2 1E-40 20 1 _nr.fas
Cannot access to folder datatemp1
perl all_seq_gr_info2.pl c:\QDD_tetetemp\sample_test_pipe2 c:\QDD_tetetemp\sample_test_pipe2 0.05 _nr.fas
perl select_unique_make_cons.pl c:\QDD_tetetemp\sample_test_pipe2 c:\QDD_tetetemp\sample_test_pipe2 win 1E-40 "C:\Program Files\iQDD\" "C:\Program Files\ClustalW2\\" 2 0.66
Cannot open temp/script_file
perl find_and_mask_ms.pl 8 4 4 4 4 4 1 0 c:\QDD_tetetemp\sample_test_pipe2 c:\QDD_tetetemp\sample_test_pipe2 _cons_plus_gr\.fas
perl group_seq_simple.pl 1E-40 "C:\Program Files\iQDD\" win c:\QDD_tetetemp\sample_test_pipe2 c:\QDD_tetetemp\sample_test_pipe2 _nr_cons_plus_gr_mask\.fas
Cannot access to folder datatemp1
c:\QDD_tetetemp\sample_test_pipe2
sample_test_pipe3.fas
The system cannot find the file specified.
0 File(s) copied
>>>>>> Sequence similarity, redundancy and sorting step done. <<<<<<
del_files = 1
flank_rep = 30
ampl_min = 90
mono_max = 4
non_mono_max = 2
min_mot_l = 2
max_mot_l = 6
min_rep = 5
primer3_path = C:\Documents and Settings\Alex Twyford\Desktop\primer3-1.1.4-WINXP\bin\
pcr_min = 90
pcr_max = 320
pcr_step = 50
min1s = 4
min2s = 2
min3s = 2
min4s = 2
min5s = 2
min6s = 2
system = win
folder = C:\Program Files\iQDD\data 2
select_pool = 1
PRIMER_GC_CLAMP = 0
PRIMER_OPT_SIZE = 20
PRIMER_MIN_SIZE = 18,PRIMER_MAX_SIZE = 27    PRIMER_OPT_TM = 60.0
PRIMER_MIN_TM = 57.0
PRIMER_MAX_TM = 63.0
PRIMER_MAX_DIFF_TM = 1000.0
PRIMER_MIN_GC = 20.0
PRIMER_OPT_GC_PERCENT = 50.0
PRIMER_MAX_GC = 80.0    PRIMER_SELF_ANY = 8.0
PRIMER_SELF_END = 3.0
PRIMER_MAX_POLY_X = 5
PRIMER_NUM_RETURN = 3
0 File(s) copied
>>>>>>>>>> Primer design step done. <<<<<<<<<<<

[Istvan Albert]

Could you please link to the source code of the programs you are running (homepage of the tool)? It might be that you are using windows and the tools was designed for unix.

Answer 1

[Neilfws]

It looks as though the program wants to use a directory (folder) named "datatemp1", which I would guess stores temporary files created during the execution of the program.

From the output, I'd guess that this folder is supposed to be located in C:Program FilesiQDD. Either it exists but the program does not have permission to write to it, or it does not exist and you need to create it.

I would also guess that this folder location is defined in one of the Perl scripts, which you could edit to point to a location that does exist and can be written to (such as C:tmp, or whatever the standard system temporary folder is on Windows).

[Istvan Albert]

Many tools have problems when the path contains spaces like the "c:Program FilesiQDD" path above.

Answer 2

[Bioch'Ti]

Hi Alex,

I have recently used iQDD to detect microsatellites in my 454 Contigs and it finally worked very well. However, I had to contact Emese Meglecz to get support. He answered me very quickly and managed to find what was wrong in my data files. Moreover, neilfws is right, iQDD is using a temporary folder which is located at c:QDD_tetetemp I guess that the program is unable to read files in this folder

Here is the link for everyone:

Regards