Can't open file [file name] , No such file or directory

dcraheem commented 4 years ago

I am new to perl. Using Strawberry perl on Windows, I have been trying to assemble the mitochondrial assembly test dataset you have provided, but keep getting this error message: "Can't open file Homo_sapiens_R1.fasta.gz, No such file or directo ry."

I got the same error message with my own data.

Here is the screen output for the test dataset:

C:\Users\draheem>perl C:\NOVOPlasty-master\NOVOPlasty3.8.3.pl -c C:\NOVOPlasty-master\config_mito_test.txt

NOVOPlasty: The Organelle Assembler Version 3.8.3 Author: Nicolas Dierckxsens, (c) 2015-2019

Input parameters from the configuration file: Verify if eve rything is correct

Project:

Project name = Homo_sapiens_test Type = mito Genome range = 12000-21000 K-mer = 39 Max memory = Extended log = Save assembled reads = Seed Input = Seed_mito.fasta Extend seed directly = Reference sequence = Variance detection = Chloroplast sequence =

Dataset 1:

Read Length = 151 Insert size = 412 Platform = illumina Single/Paired = PE Combined reads = Forward reads = Homo_sapiens_R1.fasta.gz Reverse reads = Homo_sapiens_R2.fasta.gz

Heteroplasmy:

Heteroplasmy = HP exclude list = PCR-free =

Optional:

Insert size auto = yes Insert range = 1.9 Insert range strict = 1.3 Use Quality Scores =

Can't open file Homo_sapiens_R1.fasta.gz, No such file or directo ry

C:\Users\draheem>perl -v

This is perl 5, version 30, subversion 2 (v5.30.2) built for MSWi n32-x64-multi-thread

Perl may be copied only under the terms of either the Artistic Li cense or the GNU General Public License, which may be found in the Perl 5 sour ce kit.

Complete documentation for Perl, including FAQ lists, should be f ound on this system using "man perl" or "perldoc perl". If you have acce ss to the Internet, point your browser at http://www.perl.org/, the Perl Ho me Page.

C:\Users\draheem>

Here is the config file:

config_mito_test.txt

ndierckx commented 4 years ago

Hi,

Did you gave the correct path of your seed and read files? You just gave the name of the file, but to be sure, better give the complete path

dcraheem commented 4 years ago

Thank for getting back so quickly.

I am not sure of the correct syntax, but I tried two options and got the same error message.

Please see attached config files. config_mito_test.txt config_mito_test2.txt

ndierckx commented 4 years ago

Can I see your log file?

dcraheem commented 4 years ago

Here are my screen logs: logfile2.txt logfile.txt

Currently, I have Strawberry-perl and Novoplasty-master as separate directories within my C directory.

ndierckx commented 4 years ago

Like the error said, it seems you don't give the correct path, just right click on the file and select properties, it should give you the path. And don't you ave colleagues who are more familiar with computers that can run assemblies for you?

dcraheem commented 4 years ago

I managed to solve the problem. It was not the file path; for some reason novoplasty as run on my PC doesn't like compressed data files (.fg.gz format), but works fine with the uncompressed files (.fq). I found this to be the case for your test mt genome dataset as well as my data.

ndierckx commented 4 years ago

Hi,

Could be that the perl version of Windows can't open those zipped files, now you mention I think someone had the same problem a while ago. Seem to happen with some Windows users, but I don't know the cause of that. Vast majority are linux users, there this problem never happens. Glad you found the problem

ndierckx / NOVOPlasty