gonzalezlab / t-lex3 Goto Github PK

I have installed the program, I think properly. I have tried to run it on the dataset to make sure my install is correct. However, although the script indicates that it runs completely, there are many error messages due to some missing files, that should have been created during the run.

I have tried to nail the problem and it seems that bwa is never used (nor schrimp I think). I do not think it is normal.

In particular, I do not understand, why, using the example datatest, the script never goes inside the "if" loop (below), and thus, never launches the generatefiles function, which prevents using bwa.

while (defined( my $dir = readdir (DIR4))) {
  
if ($dir !~ /\./) {
    print "\nStrain: $dir\n";
    my @files = <$inputdir/$dir/*>;
    my $filelist = join (' ', @files);
    if ($filelist =~ /\.fastq/) {
	print "$outputdir\/$dir\n"; 
	system ("mkdir $outputdir\/$dir") ; 
    	if ($binreads == 0) {
	    &generatefiles("$inputdir","$outputdir","$maxReadLength","$dir","$refgenome","$TE_map","$qual","$processes","$buffer","$junction");
   	 }
	&scorecounter("$dir","$outputdir\/$dir\/detection","$maxReadLength","$junction","$buffer","$lim","$id","$qual","$maxReadLength");
    }	
}
else{
    print "$dir\n";
}
}

here is the corresponding screen output

Strain data: /home/ubuntu/T-lex3-master/example/fastq_files/example
..
example_2.fastq
example_1.fastq
.

cat: 'tlex_example/Tpresence/*/detection/results': No such file or directory

If you have any idea, that would be great!

Hi,

I created a previous issue about a Singularity image but still face the same issues with TRF.

Is this software still supported? I am working on this for a researcher and would be keen to know if this is still supported software or if it has been deprecated, as the Github has not been updated since 2020.

Hopefully I will hear from you soon.

Thanks,
Alister

Is there a quick way to check all the pre-requisites were installed correctly and tlex3 will run properly?

Hi,

I am looking into providing this as a Singularity image for users of a HPC service.

Docker doesn't work well in clustered computing so Singularity is our best solution.

Regarding this I have converted the Dockerfile to a Singularity image, but I have persistently had issues when trying to build my image.

Firstly I have seen download problems where I can connect but not download files:

--2022-08-05 14:30:29-- (try:16) https://tandem.bu.edu/trf/downloads/trf407b.linux64
Connecting to tandem.bu.edu (tandem.bu.edu)|128.197.114.130|:443... connected.
HTTP request sent, awaiting response... Read error (Success.) in headers.
Retrying.

I have been doing more experiments today and I can't connect to that server at all and it is down on my web browser too.

--2022-10-04 10:51:13-- (try:13) http://tandem.bu.edu/trf/downloads/trf407b.linux64
Connecting to tandem.bu.edu (tandem.bu.edu)|128.197.114.130|:80... failed: Connection timed out.
Retrying.

Is this file necessary to build a working image? It seems like I can't access everything that is defined in the dockerfile.

Thanks,

Hi,

Thank you for this wonderful program.

I have noticed that in the T-lex3 pipeline, the reads were mapped to ref with BWA MEM using default options. So I was wondering that is it OK if I modified the script to skip the BWA MEM step by providing a pre-build bwa-mem.bam file? In that case, should I still provide the reads.fastq? (If the reads.fastq files were only used for bwa mapping, I would like to modify the script to get rid of these options, because I have removed my raw reads.fq after bwa mapping)

Any suggestion would be grateful.

Best wishes,

SongtaoGui