Parsnp command is not working

Question

Parsnp command is not working

smruti241 opened this issue a year ago · 20 comments

@treangen, @skoren, @dsommer, @ondovb, @MihaiPop
I ran parsnp command:
./parsnp -g GCF_000005845.2_ASM584v2_genomic.gbff GCF_003697165.2_ASM369716v2_genomic.gbff -d /home/smrutip/smruti/parsnp/genomes/*.fna -o /home/smrutip/smruti/parsnp/output -c

But I got this error:
01:17:23 - CRITICAL - The following command failed:
>>$ /home/smrutip/smruti/parsnp/bin/parsnp_core /home/smrutip/smruti/parsnp/output/parsnpAligner.ini
Please veryify input data and restart Parsnp.
If the problem persists please contact the Parsnp development team.

  STDOUT:


  STDERR:
  /bin/bash: /home/smrutip/smruti/parsnp/bin/parsnp_core: No such file or directory

Can you please tell me how to get parsnp core?

Answer 1 · 2023-04-18T20:31:13.000Z

Hi @smruti241! Thanks for opening an issue. How did you install parsnp?

Answer 2 · 2023-04-18T21:17:56.000Z

@bkille I installed all the tools mentioned in the github page "To build Parsnp from source, users must have automake 1.15, autoconf, and libtool installed. Parsnp also requires RaxML, Phipack, Harvest-tools, and numpy. Some additional features require Mash, FastANI and FastTree. All of these packages are available via Conda (many on the Bioconda channel)." Then used git clone to install. Conda command is giving error

Answer 3 · 2023-04-18T21:18:44.000Z

it would be fine if conda installation command works.

Answer 4 · 2023-04-18T21:22:23.000Z

@smruti241 and after git clone, you ran the build commands:

cd ..
./autogen.sh
./configure
make LDADD=-lMUSCLE-3.7 
make install

with no error?

Also, do you mind if I ask what the conda error was? Have your channels been set up as described here?

Answer 5 · 2023-04-18T22:04:26.000Z

yes I ran the build commands. I got error at this time. I didnt see any channels described in the github page

Answer 6 · 2023-04-18T23:28:55.000Z

Hi, what was the error you got when building?

Also, the hyperlink in the conda section of the README should take you to the Bioconda channel setup instructions. I will add a section in the README to make it more clear!

-Bryce

Answer 7 · 2023-04-19T06:09:29.000Z

it gave error 1 status while running make install

Answer 8 · 2023-04-19T06:11:29.000Z

Was there an error message? Regardless, I'd suggest setting up the bioconda channel and installing that way, should be smoother.

Answer 9 · 2023-04-19T06:12:18.000Z

so shall I uninstall and then install again?

Answer 10 · 2023-04-19T06:12:47.000Z

after setting up the bioconda channel, then I have to install parsnp using conda?

Answer 11 · 2023-04-19T06:13:52.000Z

after setting up the bioconda channel, then I have to install parsnp using conda?

Correct

Answer 12 · 2023-04-19T06:14:32.000Z

ok let me try once

Answer 13 · 2023-04-19T08:15:47.000Z

I tried to add bioconda channels and installed the parsnp using conda but this gave me error:
(parsnp) smrutip@iiitd:~/smruti$ conda install parsnp
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.

ResolvePackageNotFound:

python=3.1

Answer 14 · 2023-04-19T08:41:32.000Z

while using make install, it is giving me error:
/usr/bin/ld: cannot find -lMUSCLE-3.7
/usr/bin/ld: cannot find -lMUSCLE-3.7
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:360: parsnp_core] Error 1
make[1]: Leaving directory '/home/smrutip/smruti/parsnp/src'
make: *** [Makefile:339: all-recursive] Error 1
(parsnp) smrutip@iiitd:~/smruti/parsnp$ make install
Making install in src
make[1]: Entering directory '/home/smrutip/smruti/parsnp/src'
g++ -fopenmp -O2 -m64 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -g -O2 -fopenmp -lstdc++ -lpthread -std=gnu++0x -L/home/smrutip/anaconda3/envs/parsnp/lib -lMUSCLE-3.7 -o parsnp_core parsnp_core-MuscleInterface.o parsnp_core-parsnp.o parsnp_core-LCB.o parsnp_core-LCR.o parsnp_core-TMum.o parsnp_core-Converter.o parsnp_core-iniFile.o
/usr/bin/ld: cannot find -lMUSCLE-3.7
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:360: parsnp_core] Error 1
make[1]: Leaving directory '/home/smrutip/smruti/parsnp/src'
make: *** [Makefile:339: install-recursive] Error 1

Answer 15 · 2023-04-19T14:41:36.000Z

I tried to add bioconda channels and installed the parsnp using conda but this gave me error:

(parsnp) smrutip@iiitd:~/smruti$ conda install parsnp

Collecting package metadata (current_repodata.json): done

Solving environment: failed with initial frozen solve. Retrying with flexible solve.

Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.

ResolvePackageNotFound:

python=3.1

You'll need an environment with a much more recent version of Python. Python 3.1 was released in 2009. Try installing with an environment using Python 3.7

Answer 16 · 2023-04-19T14:44:16.000Z

while using make install, it is giving me error:

/usr/bin/ld: cannot find -lMUSCLE-3.7

/usr/bin/ld: cannot find -lMUSCLE-3.7

collect2: error: ld returned 1 exit status

make[1]: *** [Makefile:360: parsnp_core] Error 1

make[1]: Leaving directory '/home/smrutip/smruti/parsnp/src'

make: *** [Makefile:339: all-recursive] Error 1

(parsnp) smrutip@iiitd:~/smruti/parsnp$ make install

Making install in src

make[1]: Entering directory '/home/smrutip/smruti/parsnp/src'

g++ -fopenmp -O2 -m64 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -g -O2 -fopenmp -lstdc++ -lpthread -std=gnu++0x -L/home/smrutip/anaconda3/envs/parsnp/lib -lMUSCLE-3.7 -o parsnp_core parsnp_core-MuscleInterface.o parsnp_core-parsnp.o parsnp_core-LCB.o parsnp_core-LCR.o parsnp_core-TMum.o parsnp_core-Converter.o parsnp_core-iniFile.o

/usr/bin/ld: cannot find -lMUSCLE-3.7

collect2: error: ld returned 1 exit status

make[1]: *** [Makefile:360: parsnp_core] Error 1

make[1]: Leaving directory '/home/smrutip/smruti/parsnp/src'

make: *** [Makefile:339: install-recursive] Error 1

It looks like it can't find the muscle library. Did you build the muscle library with the following commands?


cd muscle
./autogen.sh
./configure --prefix=$PWD CXXFLAGS='-fopenmp'
make install

Answer 17 · 2023-04-19T16:23:49.000Z

I tried to add bioconda channels and installed the parsnp using conda but this gave me error:
(parsnp) smrutip@iiitd:~/smruti$ conda install parsnp
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
ResolvePackageNotFound:

python=3.1

You'll need an environment with a much more recent version of Python. Python 3.1 was released in 2009. Try installing with an environment using Python 3.7

I have python 3.10 version

Answer 18 · 2023-04-19T16:24:28.000Z

while using make install, it is giving me error:
/usr/bin/ld: cannot find -lMUSCLE-3.7
/usr/bin/ld: cannot find -lMUSCLE-3.7
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:360: parsnp_core] Error 1
make[1]: Leaving directory '/home/smrutip/smruti/parsnp/src'
make: *** [Makefile:339: all-recursive] Error 1
(parsnp) smrutip@iiitd:~/smruti/parsnp$ make install
Making install in src
make[1]: Entering directory '/home/smrutip/smruti/parsnp/src'
g++ -fopenmp -O2 -m64 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -g -O2 -fopenmp -lstdc++ -lpthread -std=gnu++0x -L/home/smrutip/anaconda3/envs/parsnp/lib -lMUSCLE-3.7 -o parsnp_core parsnp_core-MuscleInterface.o parsnp_core-parsnp.o parsnp_core-LCB.o parsnp_core-LCR.o parsnp_core-TMum.o parsnp_core-Converter.o parsnp_core-iniFile.o
/usr/bin/ld: cannot find -lMUSCLE-3.7
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:360: parsnp_core] Error 1
make[1]: Leaving directory '/home/smrutip/smruti/parsnp/src'
make: *** [Makefile:339: install-recursive] Error 1

It looks like it can't find the muscle library. Did you build the muscle library with the following commands?
cd muscle
./autogen.sh
./configure --prefix=$PWD CXXFLAGS='-fopenmp'
make install

yeah I used this. there was no error

Answer 19 · 2023-04-20T14:22:03.000Z

I tried to add bioconda channels and installed the parsnp using conda but this gave me error:

(parsnp) smrutip@iiitd:~/smruti$ conda install parsnp

Collecting package metadata (current_repodata.json): done

Solving environment: failed with initial frozen solve. Retrying with flexible solve.

Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.

ResolvePackageNotFound:

python=3.1

You'll need an environment with a much more recent version of Python. Python 3.1 was released in 2009. Try installing with an environment using Python 3.7

I have python 3.10 version

It looks like your conda version may need to be updated https://stackoverflow.com/a/70304326

Answer 20 · 2023-11-16T18:33:58.000Z

Hi @smruti241,

It looks like the Makefile was expecting the muscle library to be obtained from conda. I've updated the repo so that your Muscle library can be from Conda or built locally