Question: FastUniq ./Makefile gcc error
0
gravatar for SheRa
9 months ago by
SheRa0
SheRa0 wrote:

Hello, I have a MacOS Catalina - 10.15.4. Yesterday I downloaded Macports (latest version), gcc compiler (v5.5) and $gcc -v gave me the right version. Everything seems working. Downloaded fastuniq and followed the sourceforge installation page.

Open terminal window, and go to "source" folder of the FastUniq. Open the "makefile" file, go to the "GCC_OPTION" line which is used to define the compiler arguments. Your can alter it following the gcc compiler option's instructions as you needed.

When I run it, all I am getting is error:


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/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile ; exit;
(base) SheRa:~ shera$ /Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile ; exit;
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 1: fastq.h: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 2: fastq.o: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 4: -m64: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 6: all: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 8: objects: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 8: fastuniq: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 9: objects: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 9: GCC_OPTION: command not found
gcc: error: fastq_uniq.o: No such file or directory
gcc: fatal error: no input files
compilation terminated.
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 11: headers: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 11: fastq.o: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 12: GCC_OPTION: command not found
gcc: error: fastq.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 14: headers: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 14: fastq_pair.o: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 15: GCC_OPTION: command not found
gcc: error: fastq_pair.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 17: headers: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 17: fastq_pair_array.o: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 18: GCC_OPTION: command not found
gcc: error: fastq_pair_array.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 20: headers: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 20: fastq_uniq.o: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 21: GCC_OPTION: command not found
gcc: error: fastq_uniq.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 23: .PHONY: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 24: clean: command not found
/Users/shera/Desktop/Lab_Data/Download_packages/FastUniq/source/Makefile: line 25: objects: command not found
rm: fastq_uniq.o: No such file or directory
logout
Saving session...
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...saving history...truncating history files...
...completed.

[Process completed]

I appreciate any help. THanks.

ADD COMMENTlink modified 9 months ago • written 9 months ago by SheRa0
0
gravatar for ATpoint
9 months ago by
ATpoint44k
ATpoint44k wrote:

A makefile is executed by simply typing make when being in the same folder as this file. Try that.

ADD COMMENTlink written 9 months ago by ATpoint44k

I did.

(base) SheRa:source shera$ make
gcc -c fastq_uniq.c -o fastq_uniq.o -m64 -O3
fastq_uniq.c: In function 'main':
fastq_uniq.c:81:25: warning: passing argument 2 of 'getopt' from incompatible pointer type [-Wincompatible-pointer-types]
  while((ch=getopt(argc, argv, "i:t:o:p:c:"))!=-1)
                         ^
In file included from fastq_uniq.c:11:0:
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/unistd.h:509:6: note: expected 'char * const*' but argument is of type 'const char **'
 int  getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt);
      ^
gcc -o fastuniq fastq.o fastq_pair.o fastq_pair_array.o fastq_uniq.o -m64 -O3

I hope that means it is ready to be used.

ADD REPLYlink written 9 months ago by SheRa0

Is there an executable that was created? Does it run? I got the same message when compiling on Centos7 but an executable was created. Just run the tool and see if it works. If not you can always install via a package manager such as anaconda to avoid compilation from source but I guess it should be fine now.

ADD REPLYlink modified 9 months ago • written 9 months ago by ATpoint44k

I dunno, I am still trying to figure it out. I have paired end fastq.gz files, apparently I need to create a list. Why there is no proper explanatory protocol, I had no problem with trimming with trim galore but stuck @ this stage for a day now.

Edit: I have anaconda :/ Is it for real that I could have run fastuniq without downloading all these (gcc, macports) stuff?

ADD REPLYlink modified 9 months ago • written 9 months ago by SheRa0
1

Yes, that is the idea of package managers. Conda will take care of all dependencies. Still, after compilation of the above command is there an executable called fastuniq in the source folder that you can run via ./fastuniq? If so you are fine.

ADD REPLYlink written 9 months ago by ATpoint44k
0
gravatar for SheRa
9 months ago by
SheRa0
SheRa0 wrote:

If anyone will have a problem with FastUniq, let me tell you what I have done to make it work:

to run the fastuniq with command line: go to the file path .../fastuniq/source

ls site1_R1_P.fq site1_R2_P.fq > input_list.txt

by this command you will create a txt file that your file names are written in. example: R24_2033_S1_L001_R1_001_val_1.fq R24_2033_S1_L001_R2_001_val_2.fq

  • Then I extracted the files to the same location (fastuniq/source) in where input_list.txt file is [I am sure there is other ways of doing , maybe pwd]
  • Run the code:

    fastuniq -i input_list.txt -t q -o output_1.fastq -p output_2.fastq -c 1

ADD COMMENTlink written 9 months ago by SheRa0
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