seqtk about seqtk HOT 23 CLOSED

@idjoly - try passing the flag -lm, telling gcc to link against the math lib.

from seqtk.

You mean instead of -lz?

/tmp/ccdlG3x7.o: In function ks_getc': seqtk.c:(.text+0xe0): undefined reference togzread'
/tmp/ccdlG3x7.o: In function ks_getuntil2': seqtk.c:(.text+0x1f3): undefined reference togzread'
/tmp/ccdlG3x7.o: In function stk_reg_read': seqtk.c:(.text+0x15b8): undefined reference togzopen'
seqtk.c:(.text+0x15d5): undefined reference to gzdopen' seqtk.c:(.text+0x1889): undefined reference togzclose'
/tmp/ccdlG3x7.o: In function stk_revseq': seqtk.c:(.text+0x19db): undefined reference togzopen'
seqtk.c:(.text+0x19f8): undefined reference to gzdopen' seqtk.c:(.text+0x1b7b): undefined reference togzclose'
/tmp/ccdlG3x7.o: In function stk_trimfq': seqtk.c:(.text+0x1c98): undefined reference togzopen'
seqtk.c:(.text+0x1cb5): undefined reference to gzdopen' seqtk.c:(.text+0x2031): undefined reference togzclose'
/tmp/ccdlG3x7.o: In function stk_comp': seqtk.c:(.text+0x215a): undefined reference togzdopen'
seqtk.c:(.text+0x217f): undefined reference to gzopen' seqtk.c:(.text+0x259e): undefined reference togzclose'
/tmp/ccdlG3x7.o: In function stk_randbase': seqtk.c:(.text+0x2620): undefined reference togzdopen'
seqtk.c:(.text+0x263a): undefined reference to gzopen' seqtk.c:(.text+0x280d): undefined reference togzclose'
/tmp/ccdlG3x7.o: In function stk_hety': seqtk.c:(.text+0x29a1): undefined reference togzdopen'
seqtk.c:(.text+0x29c3): undefined reference to gzopen' seqtk.c:(.text+0x2c8d): undefined reference togzclose'
/tmp/ccdlG3x7.o: In function stk_fq2fa': seqtk.c:(.text+0x2da5): undefined reference togzopen'
seqtk.c:(.text+0x2dc2): undefined reference to gzdopen' seqtk.c:(.text+0x2f7f): undefined reference togzclose'
/tmp/ccdlG3x7.o: In function stk_maskseq': seqtk.c:(.text+0x30e9): undefined reference togzopen'
seqtk.c:(.text+0x3106): undefined reference to gzdopen' seqtk.c:(.text+0x34db): undefined reference togzclose'
/tmp/ccdlG3x7.o: In function stk_subseq': seqtk.c:(.text+0x3610): undefined reference togzopen'
seqtk.c:(.text+0x362d): undefined reference to gzdopen' seqtk.c:(.text+0x3989): undefined reference togzclose'
/tmp/ccdlG3x7.o: In function stk_mergefa': seqtk.c:(.text+0x3b99): undefined reference togzopen'
seqtk.c:(.text+0x3bb6): undefined reference to gzdopen' /tmp/ccdlG3x7.o: In functionstk_famask':
seqtk.c:(.text+0x40a7): undefined reference to gzopen' seqtk.c:(.text+0x40c4): undefined reference togzdopen'
/tmp/ccdlG3x7.o: In function stk_mutfa': seqtk.c:(.text+0x43a1): undefined reference togzopen'
seqtk.c:(.text+0x43be): undefined reference to gzdopen' seqtk.c:(.text+0x460b): undefined reference togzclose'
seqtk.c:(.text+0x465b): undefined reference to gzopen' seqtk.c:(.text+0x4678): undefined reference togzdopen'
seqtk.c:(.text+0x4809): undefined reference to gzclose' /tmp/ccdlG3x7.o: In functionstk_listhet':
seqtk.c:(.text+0x491e): undefined reference to gzdopen' seqtk.c:(.text+0x4938): undefined reference togzopen'
seqtk.c:(.text+0x49f1): undefined reference to gzclose' /tmp/ccdlG3x7.o: In functionstk_cutN':
seqtk.c:(.text+0x4e0b): undefined reference to gzdopen' seqtk.c:(.text+0x4e2d): undefined reference togzopen'
seqtk.c:(.text+0x4f16): undefined reference to gzclose' /tmp/ccdlG3x7.o: In functionstk_hrun':
seqtk.c:(.text+0x4feb): undefined reference to gzdopen' seqtk.c:(.text+0x500d): undefined reference togzopen'
seqtk.c:(.text+0x5144): undefined reference to `gzclose'
collect2: ld returned 1 exit status

from seqtk.

No, in addition to lz. kseq.h needs zlib.

from seqtk.

Then, nothing happened. No error. But seqtk is not working...

from seqtk.

Why are you cloning that repo? Try just git clone git://github.com/lh3/seqtk.git && (cd seqtk && make)

from seqtk.

But there is no Makefile!?

from seqtk.

There is a makefile: https://github.com/lh3/seqtk/blob/master/Makefile.

from seqtk.

Looks like I had a different repo (outdated?) misc.git instead of seqtk.git

Now this is what I get...

david@david-P6T-AS[seqtk] sudo make
gcc -g -Wall -O2 seqtk.c -o seqtk -lz -lm
seqtk.c: In function ‘stk_comp’:
seqtk.c:277:16: warning: variable ‘lc’ set but not used [-Wunused-but-set-variable]

from seqtk.

That's just a warning — unused variables are safe to ignore.

from seqtk.

Ok, it is working... but now I'm looking for the fq2fa function!?

In fact I am running a script (not made by me) which at some point call "seqtk fq2fa". I had seqtk working (don't remember where I got it) but fq2fa was not part of it, so I thought there was a new version. Now I am somewhat confused...

from seqtk.

Well, if the script can't find seqtk, as in seqtk is not in your $PATH, then that's why it's not working. Does running just ./seqtk in the seqtk directory work?

from seqtk.

Yes, sorry about that. See my updated comment...

from seqtk.

fq2fa is a subcommand — I suggest spending some time familiarizing yourself with the README.md file.

from seqtk.

I know that... but the command is not working

david@david-P6T-AS[Race9] seqtk fq2fa Race9.fq 20 > Race9.fa
[main] unrecognized commad 'fq2fa'. Abort!

from seqtk.

What does running seqtk alone (no arguments) give you?

from seqtk.

david@david-P6T-AS[Race9] seqtk

Usage: seqtk

Command: seq common transformation of FASTA/Q
comp get the nucleotide composition of FASTA/Q
sample subsample sequences
subseq extract subsequences from FASTA/Q
trimfq trim FASTQ using the Phred algorithm
hety regional heterozygosity
mutfa point mutate FASTA at specified positions
mergefa merge two FASTA/Q files
randbase choose a random base from hets
cutN cut sequence at long N
listhet extract the position of each het

from seqtk.

Huh, maybe this version is out of date. I see it in the one from misc.
Just use that.

On Thu, Feb 14, 2013 at 2:40 PM, David Joly [email protected]:

david@david-P6T-AS[Race9] seqtk

Usage: seqtk

Command: seq common transformation of FASTA/Q
comp get the nucleotide composition of FASTA/Q
sample subsample sequences
subseq extract subsequences from FASTA/Q
trimfq trim FASTQ using the Phred algorithm
hety regional heterozygosity
mutfa point mutate FASTA at specified positions
mergefa merge two FASTA/Q files
randbase choose a random base from hets
cutN cut sequence at long N
listhet extract the position of each het

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/6#issuecomment-13582954.

Vince Buffalo
Bioinformatics Programmer
Dubcovsky Lab
Plant Sciences, UC Davis

from seqtk.

But then, we're back to the beginning... there is no Makefile in the seqtk from misc!

Where do you see fq2fa?

from seqtk.

Arghhh, I'm such a noob! Ok I got it now!

Thanks a million time Vince!

P.S. So you're in Dubcovsky lab heh, say hello to Ksenia!

from seqtk.

Excellent — how? With which repository?

from seqtk.

The misc repository... using the gcc command, but then not forgetting about copying the file in the bin directory (or using ./seqtk from within the directory)

from seqtk.

Excellent! Glad it worked. When I have some free time I'll check why this repository is different than that one.

from seqtk.

Misc/seqtk is very old. Several commands have been merged to a single seq command. Please read the readme.

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