Can't locate IO/Zlib.pm

[GoogleCodeExporter]

What steps will reproduce the problem?
1. I could not run the condetri perl script

What is the expected output? What do you see instead?
Received an error message that it could not locate "Can't locate IO/Zlib.pm in 
@INC"
Install the IO-Zlib-1.09 but still get the same message 

What version of the product are you using? On what operating system?
Latest version on fedora

Please provide any additional information below.

Original issue reported on code.google.com by raimired...@gmail.com on 3 May 2013 at 1:38

[GoogleCodeExporter]

This problem is solved now! But after running the condetri on my sequence, the 
prefix_trim1.fastq is emptied! there is nothing on the file and I used this 
command:

       perl ~/Raimi/Perl_Script/condetri_v2.2.pl fastq1=seq_3_1.fq fastq2=seq_3_2.fq -prefix=1

Please, need help!

Original comment by raimired...@gmail.com on 4 May 2013 at 4:33

[HilbigA]

Hi I am having the exact same problems: request to load the IO:Zlib, despite the version claiming to use zcat. When I run it on a unzipped fastq, the trimmed read file has 0 bytes. I have tried both on ubuntu (CLIMB) and an iOS, same results. Thanks for any ideas

[linneas]

Hello,

Do you get any output at all (text to stdout)? It should write how many reads have been processed/trimmed. If you get output but it trims away 100% of the sequences, maybe it's something with the settings, for example wrong scoring table is used (-sc flag, 64 or 33 depending on what version of Illumina reads you have).

I'm unfortunately not actively maintaining ConDeTri anymore and haven't trimmed reads in a long time, but I guess there might be other, more modern software around..

However, if you still want to use ConDeTri I can try debugging, but then I need the full command you used to run it, plus an example of your data (first 10 reads or so, from both pairs if you're using paired end data).

Best wishes, Linnéa

[HilbigA]

Dear Linnéa,

Thank you so much, I appreciate your response and offer to help out, especially understanding that you don’t actively maintain condetri any longer.

Your advice on using a 33 score rather than 64 did the trick, I was using the wrong setting.

I am sorry to have bothered you with this, I am entirely new to read processing and stumbling around a bit still.

Warm regards, Antonia

From: Linnéa Smeds @.> Date: Friday, 17. March 2023 at 13:06 To: linneas/condetri @.> Cc: Antonia Hilbig (PGR) @.>, Comment @.> Subject: Re: [linneas/condetri] Can't locate IO/Zlib.pm (#2)

Hello,

Do you get any output at all (text to stdout)? It should write how many reads have been processed/trimmed. If you get output but it trims away 100% of the sequences, maybe it's something with the settings, for example wrong scoring table is used (-sc flag, 64 or 33 depending on what version of Illumina reads you have).

I'm unfortunately not actively maintaining ConDeTri anymore and haven't trimmed reads in a long time, but I guess there might be other, more modern software around..

However, if you still want to use ConDeTri I can try debugging, but then I need the full command you used to run it, plus an example of your data (first 10 reads or so, from both pairs if you're using paired end data).

Best wishes, Linnéa

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