step 2 fails, permission denied

[dcopetti]

Hello, I was not able to run successfully SINE_Scan on a subset of my assembly (for testing purposes). The command I used was: perl SINE_Scan_process.pl -s 123 -g /path/subset.fa -o /path/test_id2 -d /path/subset_run/ the bottom of the stdout reads:

Maximum file size: 1000000000B
Adding sequences from FASTA; added 250 sequences in 8.71143 seconds.
Modification of non-creatable array value attempted, subscript -1 at /home/copettid/bin/SINE_Scan/SINE_Scan-v1.1.1/PL_pipeline/RG_boundary.pl line 117, <GEN1> line 48.
Time cost for Boundary fix:29126 wallclock secs ( 0.00 usr  0.00 sys + 29708.38 cusr 1494.27 csys = 31202.65 CPU)
Step Two: SINE Verification.
Permission denied
Permission denied
Permission denied
Permission denied
Permission denied
Permission denied
Permission denied
Permission denied
Permission denied
Permission denied
Permission denied
Permission denied
Permission denied
Permission denied
Permission denied
Finish Step Two.
Time cost for Module Two :111 wallclock secs ( 0.00 usr  0.00 sys + 107.27 cusr  6.12 csys = 113.39 CPU)
Step Three: Cannot read validated SINE candidate file. Stop.
If you ran Step 2, please check the file with the suffix of for_annotation.fa. Empty file means no good candidate was identified.
If you use your own validated SINEs (-a parameter), check this file.

and the output folder has:

-rw-r--r-- 1 copettid mpb 620M May 18 11:42 subset.fasta
-rw-r--r-- 1 copettid mpb 111K May 18 13:08 subset-5smatches.fasta
-rw-r--r-- 1 copettid mpb 1.2M May 18 13:37 subset-matches.fasta
-rw-r--r-- 1 copettid mpb 156M May 18 13:37 subset.fasta.nsq
-rw-r--r-- 1 copettid mpb 3.1K May 18 13:37 subset.fasta.nin
-rw-r--r-- 1 copettid mpb  19K May 18 13:37 subset.fasta.nhr
-rw-r--r-- 1 copettid mpb 8.4K May 18 21:42 subset.sine.fa
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:42 0
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:43 1
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:43 2
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:43 6
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:43 9
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:43 10
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:43 11
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:43 12
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:43 13
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:43 15
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:43 16
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:43 19
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:44 21
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:44 25
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:44 26
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:44 27
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:44 30
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:44 33
-rw-r--r-- 1 copettid mpb  16K May 18 21:44 subset.moduleTwo.logfile
drwxr-xr-x 2 copettid mpb 4.0K May 18 21:44 34

with the .log file not showing any error or issue. What is the reason for my failed run? Can it be the too small input size (10% of the assembly)? Do I need to change permissions somewhere? Thanks, Dario

[dcopetti]

Hi,

I think I found the issue, the parameters had to go at the end of the command.

[uceleste]

Hi Dario,

I have exactly the same problem but can not solve it. What do you mean when you say to put the parameters at the end of the command? Something like this? Just putting "-s 123" at the end?

perl SINE_Scan_process.pl -g subset.fa -o test -d /path/subset.fa -s 123

[dcopetti]

Hi @uceleste,

correct, that is what I did. I don't remember exactly the command now, but it was something like perl SINE_Scan_process.pl -g /path/to/genome.fasta -o /path/to/test_id2 -d /path/to/mockfolder -s 123 –k 1 and it was run from the folder where the perl is (in case it may have a meaning).

[uceleste]

Thank you very much @dcopetti, it works now!

[Ramkyeri]

@dcopetti

Hi I am getting the error, coudl you give some suggestion?

------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Could not read file '/media/data/ramakrishnan/workspace/testProject/sinescan/result/RG/1903/1903.sine.extendseq.msa.fasta': No such file or directory STACK: Error::throw STACK: Bio::Root::Root::throw /home/ram/transposon_annotation_tools_env/lib/site_perl/5.26.2/Bio/Root/Root.pm:447 STACK: Bio::Root::IO::_initialize_io /home/ram/transposon_annotation_tools_env/lib/site_perl/5.26.2/Bio/Root/IO.pm:268 STACK: Bio::AlignIO::_initialize /home/ram/transposon_annotation_tools_env/lib/site_perl/5.26.2/Bio/AlignIO.pm:401 STACK: Bio::AlignIO::new /home/ram/transposon_annotation_tools_env/lib/site_perl/5.26.2/Bio/AlignIO.pm:311 STACK: Bio::AlignIO::new /home/ram/transposon_annotation_tools_env/lib/site_perl/5.26.2/Bio/AlignIO.pm:332 STACK: main::Similarity /home/ram/transposon_annotation_tools_env/bin/SINE_Scan-v1.1.1//PL_pipeline/RG_boundary.pl:205 STACK: /home/ram/transposon_annotation_tools_env/bin/SINE_Scan-v1.1.1//PL_pipeline/RG_boundary.pl:22