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phasegenomics / FALCON-Phase

FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds
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zlib.h: no such file #64

Closed olechnwin closed 5 years ago

olechnwin commented 5 years ago

Hi,

I am trying to install falcon-phase but when I do git clone --recursive https://github.com/phasegenomics/FALCON-Phase.git ; cd FALCON-Phase/src ; make

I got the following error:

cd ../htslib && make
make[1]: Entering directory `/gpfs0/home/cxt050/opt/FALCON-Phase/htslib'
gcc -g -Wall -O2 -I.  -c -o bgzf.o bgzf.c
In file included from bgzf.c:39:0:
htslib/bgzf.h:35:10: fatal error: zlib.h: No such file or directory
 #include <zlib.h>
          ^~~~~~~~
compilation terminated.
make[1]: *** [bgzf.o] Error 1
make[1]: Leaving directory `/gpfs0/home/cxt050/opt/FALCON-Phase/htslib'
make: *** [../htslib/libhts.a] Error 2

I have installed all the dependencies listed. Please let know what I need to do. Thank you!

shawnpg commented 5 years ago

Hi,

Have you tried installing via PacBio's conda environment https://github.com/PacificBiosciences/pbbioconda? Official support for FALCON-Phase has moved there and it's usually much easier to get the environment up and running. If that won't work for you, let us know and we'll investigate.

Thanks!

olechnwin commented 5 years ago

@shawnpg thank you so much for your quick reply. I haven't tried PacBio's conda environment. I'll try it and post back. Thanks!

olechnwin commented 5 years ago

@shawnpg, Sorry. I don't really understand how to install FALCON-Phase using PacBio's conda environment. I don't see FALCON-Phase on the list of packages. Do I install pb-assembly?

shawnpg commented 5 years ago

Hi,

It's included in the pb-falcon package. Sorry I didn't mention it. It's buried in the release notes (https://github.com/PacificBiosciences/pbbioconda/wiki/Release-notes), but it's there as of January.

Thanks!

olechnwin commented 5 years ago

I've installed the entire pb-assembly which also includes falcon-phase package. How do I run it the test dataset? Do I still follow the readme in this page? Do I still clone the repo and use the test data, config.sh and config.json? If I do need to follow the readme, then I need to install snakemake as it is not installed with pb-assembly.

Thanks!

zeeev commented 5 years ago

Hi @olechnwin,

Currently there is no documentation for running FALCON-Phase with pb-assembly. I'm still recommending that people use this repository since it has been extensively tested and continually supported.

The original error you reported is that a system library is missing. The zlib library is required by htslib. If you have samtools installed on your system chances are that you've also installed htslib. FALCON-phase uses htslib to read the bam files.

Sorry for the confusion.

--Zev

olechnwin commented 5 years ago

Ok. I was able to fix the library error by loading gcc 7.2.0 library before compiling.

I ran the test dataset and have the following warning:

Warning: error in phasing, did you run enough iterations ('iter' >= 10e6)? 000000F_001:0-26421 and 000000F:10327801-10353990 'phased.txt' contains '-nan'
Warning: error in phasing, did you run enough iterations ('iter' >= 10e6)? 000000F_003:0-35964 and 000000F:21633239-21669154 'phased.txt' contains '-nan'

Is it supposed to throw this warning? What does it mean?

zeeev commented 5 years ago

Hi @olechnwin,

We updated the default number of permutations required. I didn't update the sample config. If you increase the number of iterations you should be good.