Installation error

[rugilemat]

Hi, I seem to be having a similar error as #1096:

/usr/bin/ld: cannot find -lbz2
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:316: libhts.so] Error 1
make[1]: Leaving directory '/users/k1347718/nanopolish/htslib'
make: *** [Makefile:139: htslib/libhts.a] Error 255

I have also tried installing through conda but get:

nanopolish: error while loading shared libraries: libhdf5.so.10: cannot open shared object file: No such file or directory

The above error happens regardless whether I install it through git or conda. I tried installing the lbz2 package separately but that didn't seem to help so any advice would be appreciated.

[Modernism-01]

Hello, I had the same problem. Did you solve it?

[rugilemat]

No @Modernism-01, I'm still struggling with it.

[rdeborja]

Issue #1071 seems to have addressed this.

Nanopolish requires htslib, which in turn requires a library called bz2
(this is the -lbz2 error). You'll need to install this to compile both.

When you tried installing the bz2 library manually, did you update all the necessary environment variables to point to it? Also, what operating system are you using?

[rugilemat]

I've been trying to use the system-wide ones we have installed on the HPC, so they should be loaded to the path and run the command: make HDF5=noinstall HTS=noinstall

This is what I end up with after letting the make run till the end:

make[1]: Leaving directory '/scratch/prj/ppn_microglia_mod/directrna/scripts/nanopolish/slow5lib'
g++ -o nanopolish -g -O3 -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64    -I./minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -I./eigen/ -I./slow5lib/include/ -fPIC src/main/nanopolish.o src/nanopolish_vcf2fasta.o src/nanopolish_polya_estimator.o src/nanopolish_haplotype.o src/nanopolish_call_methylation.o src/nanopolish_squiggle_read.o src/nanopolish_detect_polyi.o src/nanopolish_variant_db.o src/nanopolish_read_db.o src/nanopolish_methyltrain.o src/nanopolish_raw_loader.o src/nanopolish_index.o src/nanopolish_scorereads.o src/training_core.o src/nanopolish_phase_reads.o src/nanopolish_fast5_check.o src/nanopolish_call_variants.o src/nanopolish_train_poremodel_from_basecalls.o src/hmm/nanopolish_transition_parameters.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r9.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_klcs.o src/common/nanopolish_alphabet.o src/common/nanopolish_iupac.o src/common/nanopolish_common.o src/common/nanopolish_variant.o src/common/nanopolish_bam_utils.o src/common/nanopolish_bam_processor.o src/alignment/nanopolish_eventalign.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_alignment_db.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/io/nanopolish_fast5_processor.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_io.o src/basemods/nanopolish_basemods.o src/thirdparty/fet.o src/thirdparty/stdaln.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o  ./minimap2/libminimap2.a ./slow5lib/lib/libslow5.a  -lz -lrt -lhdf5 -lhts 

And while it doesn't seem like it ends up with any errors, I still end up with:

Command 'nanopolish' not found, but can be installed with:

apt install nanopolish
Please ask your administrator.
You will have to enable the component called 'universe'

So I'm really not sure what I'm doing wrong or what's going on.

[rdeborja]

@rugilemat is there nanopolish in the directory somewhere if you run the following? find . -name nanopolish It should be in the root directory where you ran the make command.

[rugilemat]

Yeah I can find it in the nanopolish folder and that's where I tried to run it from when I got that error.

Here's how the nanopolish folder looks like:

DEVELOPERS.md   docs                 etc      Makefile    README.md  src
Dockerfile      eigen                htslib   minimap2    scripts    test
Dockerfile-arm  eigen-3.3.7.tar.bz2  LICENSE  nanopolish  slow5lib

But it won't let me run it.

[rdeborja]

@rugilemat can you try running ./nanopolish instead of nanopolish?

[rugilemat]

Thanks - currently trying to run ./nanopolish index and it seems to be working.

But so far it seems like the way to solve the error

collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:316: libhts.so] Error 1
make[1]: Leaving directory '/users/k1347718/nanopolish/htslib'
make: *** [Makefile:139: htslib/libhts.a] Error 255

was running make HDF5=noinstall HTS=noinstall and loading locally installed libraries instead.

I'll see if I can get through ./nanopolish index and close the issue if that functions.

[rdeborja]

Glad it seems to be working although I'm still a bit confused on the original error. I've been building from scratch (including htslib and hdf5) and haven't been able to reproduce the error.

[rugilemat]

I think I'll have to reinstall as I can run nanopolish index but getting errors in nanopolish eventalign with multithreading and VBZ compression support (the HDF5 and HTS libraries we got installed on the cluster are too old for that.

I'll try to build from scratch again and see if error persists or if there is some other way I can install those libraries.

[rugilemat]

I tried building from scratch and the error persists:

gcc -shared -Wl,-soname,libhts.so.3 -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico -lz -lm -lbz2 -lpthread
/usr/bin/ld: cannot find -lbz2
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:316: libhts.so] Error 1
make[1]: Leaving directory '/scratch/prj/ppn_microglia_mod/directrna/scripts/nanopolish/htslib'
make: *** [Makefile:139: htslib/libhts.a] Error 255

I'm looking into alternative ways for installing libraries.

[hasindu2008]

You can try doing a minimal hts build using the script at https://github.com/hasindu2008/f5c/blob/master/scripts/install-hts.sh. Then perhaps point the nanopolish to this htslib build.

[rugilemat]

Thanks @hasindu2008 - looks like it's missing lbz2 so I need to find a way to install that first.

[hasindu2008]

If you specify --enable-bz2=no --enable-lzma=no to the configure step of htslib, lbz2 is not required.

[rugilemat]

I managed to get it running by installing it through conda. However, I am having some trouble with my fast5 files as eventalign gives no output.