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I ran pairfq on several fastq.gz files and for some (but not all of them) I am getting the following error:
"ERROR: Could not open file: /folder/file_f.fastq.gz"

However, I am able to do "zcat /folder/file_f.fastq.gz | head" and the file is there. I cannot detect any obvious differences between the files that do run and the ones that give this message. Any idea as to what would cause this?

Thank you

hello i have a fastq file which is not inter leafed it has around 1 million sequences with first half million forward rest half million reverse can you please suggest me how to seperate them using pairfq

It would be nice for many applications if you could write to stdout instead of a file.

Program hangs forever waiting for input from stdin when files contain a dash. Need to rework get_fh() method.

When I apply pairfq addinfo to trim-galore-cleaned-reads (8.8GB) I obtain outputs with a weight of 4.4GB. What could be the reason of this?

perl pairfq addinfo -i sample1.fq -o sample1_pairinfo.fq -p 1

perl pairfq addinfo -i sample2.fq -o sample2_pairinfo.fq -p 2

After that, if I use pairinfo makepairs, the program does not find any paired read in the samples:

perl pairfq makepairs -f sample1_pairinfo.fq -r sample2_pairinfo.fq -fp for_paired.fq -rp rev_paired.fq -fs for_unpaired.fq -rs rev_unpaired.fq

Currently, the default is to add ".gz" to gzipped files when compressing the output (and similarly for bzip2), but the file names should be checked instead of doing this naively. It is unnatural to specify a file name and have the name changed.

This option is available when pairing reads from separate files, but currently it is unavailable when pairing reads from an interleaved file.

The input to pairfq makepairs currently is separate files of forward and reverse reads. If the input is interleaved, it would be necessary to split them with pairfq splitpairs first before pairing. The added benefit of pairing from interleaved files is reduced memory usage for large numbers of reads.

Hi

I noticed that when the -c 'gzip' flag is turned on we get an exception (see below), could this be fixed please :)

Thank you

[hraaxt@genomex]$ perl /software/x86_64/Pairfq/bin/pairfq makepairs -c 'gzip' -f 05.seqClean/RS_1_no_hits.fastq -r 05.seqClean/RS_2_no_hits.fastq -fp RS_no_hits_pe_1.fastq -rp RS_no_hits_pe_2.fastq -fs RS_no_hits_se_1.fastq -rs RS_no_hits_se_2.fastq
Use of uninitialized value $_[1] in string eq at
        /software/share/lib/perl/lib/perl5/x86_64-linux-thread-multi/IO/Compress/Base/Common.pm line 280 (#1)
    (W uninitialized) An undefined value was used as if it were already
    defined.  It was interpreted as a "" or a 0, but maybe it was a mistake.
    To suppress this warning assign a defined value to your variables.

    To help you figure out what was undefined, perl will try to tell you the
    name of the variable (if any) that was undefined. In some cases it cannot
    do this, so it also tells you what operation you used the undefined value
    in.  Note, however, that perl optimizes your program and the operation
    displayed in the warning may not necessarily appear literally in your
    program.  For example, "that $foo" is usually optimized into "that "
    . $foo, and the warning will refer to the concatenation (.) operator,
    even though there is no . in your program.

Uncaught exception from user code:
        IO::Compress::Gzip::gzip: output filename is undef or null string at /software/x86_64/Pairfq/bin/pairfq line 571.
 at /software/share/lib/perl/lib/perl5/x86_64-linux-thread-multi/IO/Compress/Base/Common.pm line 353.
        IO::Compress::Base::Validator::croakError(IO::Compress::Base::Validator=HASH(0x7fe9477cc8c8), "IO::Compress::Gzip::gzip: output filename is undef or null st"...) called at /software/share/lib/perl/lib/perl5/x86_64-linux-thread-multi/IO/Compress/Base/Common.pm line 326
        IO::Compress::Base::Validator::new("IO::Compress::Base::Validator", "IO::Compress::Gzip", SCALAR(0x23d5b78), "IO::Compress::Gzip::gzip", "RS_no_hits_pe_1.fastq", undef) called at /software/share/lib/perl/lib/perl5/x86_64-linux-thread-multi/IO/Compress/Base.pm line 343
        IO::Compress::Base::_def(IO::Compress::Gzip=GLOB(0x7fe9477d52b0), "RS_no_hits_pe_1.fastq") called at /software/share/lib/perl/lib/perl5/x86_64-linux-thread-multi/IO/Compress/Gzip.pm line 51
        IO::Compress::Gzip::gzip("RS_no_hits_pe_1.fastq") called at /software/x86_64/Pairfq/bin/pairfq line 571
        main::compress("gzip", "RS_no_hits_pe_1.fastq", "RS_no_hits_pe_2.fastq", "RS_no_hits_se_1.fastq", "RS_no_hits_se_2.fastq") called at /software/x86_64/Pairfq/bin/pairfq line 268
        main::make_pairs_and_singles("pairfq", "05.seqClean/RS_1_no_hits.fastq", "05.seqClean/RS_2_no_hits.fastq", "RS_no_hits_pe_1.fastq", "RS_no_hits_pe_2.fastq", "RS_no_hits_se_1.fastq", "RS_no_hits_se_2.fastq", undef, "gzip", ...) called at /software/x86_64/Pairfq/bin/pairfq line 136
        main::makepairs(HASH(0x2373c70), HASH(0x1d361f0), "pairfq") called at /software/x86_64/Pairfq/bin/pairfq line 75

Hi to all,

I am trying to use meRanGs align program and I achieve the following error when I run the program:

ERROR SRR3583357_1_trimmed.fq and SRR3583357_2_trimmed.fq are not properly paired, you may use pairfq (S. Evan Staton) tool to pair and sort the mates at script/meRanGs.pl line 4149, <GEN10> line 4.

So now, I am trying to use pairfq program. In this case I have forward reads and reverse reads obtained after trimming with trim galore so I am runing the following line:

perl pairfq makepairs -f ~/SRR3583357_1.fastq_trimming_report.txt -r ~/SRR3583357_2.fastq_trimming_report.txt
and all the time I obtained the following error:

ERROR: Command line not parsed correctly. Check input.
I saw thar there are various options that are required in the program but I only have two inputs, one with the forward paired reads and other with the reverse ones, so I do not know what other files I have to use as input.

Thank you to all, I hope somebody could help me.
Vera

Hey, so I'm tryng to install in an ubuntu subsystem (windows WSL).

When using command:
sudo curl -sL cpanmin.us | sudo perl - git://github.com/sestaton/Pairfq.git

I get an error:

Cloning git://github.com/sestaton/Pairfq.git ... FAIL
! Failed cloning git repository git://github.com/sestaton/Pairfq.git
! Couldn't find module or a distribution git://github.com/sestaton/Pairfq.git

I've tried downloading and installing latest version using: perl Makefile.PL

And I get the error:

Warning: prerequisite Tie::Hash::DBD 0.13 not found.
Generating a Unix-style Makefile
Writing Makefile for Pairfq
Unable to open MakeMaker.tmp: Permission denied at /usr/share/perl/5.34/ExtUtils/MakeMaker.pm line 1225.

I would really appreciate the help.

Best regards,

Old versions will not recognize the parameters used for creating makefile:

$ perl Makefile.PL 
WARNING: MIN_PERL_VERSION is not a known parameter.
WARNING: CONFIGURE_REQUIRES is not a known parameter.
WARNING: BUILD_REQUIRES is not a known parameter.
WARNING: LICENSE is not a known parameter.
Checking if your kit is complete...
Looks good
Warning: prerequisite BerkeleyDB 0.54 not found.
Warning: prerequisite IPC::System::Simple 1.21 not found.
Warning: prerequisite List::MoreUtils 0.33 not found.
'BUILD_REQUIRES' is not a known MakeMaker parameter name.
'CONFIGURE_REQUIRES' is not a known MakeMaker parameter name.
'LICENSE' is not a known MakeMaker parameter name.
'MIN_PERL_VERSION' is not a known MakeMaker parameter name.
Writing Makefile for bin/pairfq

Need to check version of ExtUtils::MakeMaker before trying to write makefile.

I think it would gain some traction and be a good addition over there!

Cheers,

Seb

Hello, I installed Pairfq over internet and the installation itself is fine and Pairfq work perfectly, but the problem is the database location. How can I change the location to another physical disk? My fastq-files are extreme large and for that reason I have all data on another disk. Pairfq creates the working database on system disk which is not large enough to handle billions reads.