Compiled Parsnp-OSX64-v1.2.tar, hangs and errors, OS X 10.12 issue?

[sconlan]

After updating my Mac to OS X 10.12.6, I downloaded the binary for parsnp and tried to run previously working commands. First issue is that the help page takes over a minute to display:

sh-3.2$ time ./Parsnp-OSX64-v1.2/parsnp                                                                           
|--Parsnp v1.2--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
usage: parsnp [options] [-g|-r|-q](see below) -d <genome_dir> -p <threads>

Parsnp quick start for three example scenarios: 
1) With reference & genbank file: 
...
 -P = <int>: max partition size? limits memory usage (default= 15000000)
 -v = <flag>: (v)erbose output? (default = NO)
 -V = <flag>: output (V)ersion and exit

real    1m14.101s
user    1m10.017s
sys     0m0.621s

Second, previously working commands error like:

sh-3.2$ time ./Parsnp-OSX64-v1.2/parsnp -c -x -p 4 -r Mvel_NIH1002.PB_DATA.canu.SK.fasta -d ./genomes/            
|--Parsnp v1.2--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
***********************************************************************************
SETTINGS:
|-refgenome:    Mvel_NIH1002.PB_DATA.canu.SK.fasta
|-aligner:      libMUSCLE
|-seqdir:       ./genomes/
|-outdir:       /Users/conlans/Desktop/Mucor_parsnp_redo/P_2018_05_07_140352716154
|-OS:           Darwin
|-threads:      4
***********************************************************************************

<<Parsnp started>>

-->Reading Genome (asm, fasta) files from ./genomes/..
  |->[OK]
-->Reading Genbank file(s) for reference (.gbk) ..
  |->[WARNING]: no genbank file provided for reference annotations, skipping..
-->Running Parsnp multi-MUM search and libMUSCLE aligner..
**ERROR**
The following command failed:
>>/var/folders/h5/kzbqz8hs5dz1q1234dltgkxh0pbxfz/T/_MEICrRy19/parsnp /Users/conlans/Desktop/Mucor_parsnp_redo/P_2018_05_07_140352716154/parsnpAligner.ini
Please veryify input data and restart Parsnp. If the problem persists please contact the Parsnp development team.
**ERROR**

real    1m20.935s
user    1m14.233s
sys     0m1.290s

[sconlan]

Actually, I'm having the same problem on a Linux system with the compiled version. The data and commandline args are the same ones that have worked in the past:

10:30 cn3115 Muc_PARSnp$ ../../../bin/Parsnp-Linux64-v1.2/parsnp -c -x -p 4 -r Mvel_NIH1002.PB_DATA.canu.SK.fasta -d ./genomes/
|--Parsnp v1.2--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
****************************************************************************************************************
SETTINGS:
|-refgenome:    Mvel_NIH1002.PB_DATA.canu.SK.fasta
|-aligner:      libMUSCLE
|-seqdir:       ./genomes/
|-outdir:       /gpfs/gsfs4/users/Segrelab/Mucor2017/results/parsnp_genome/Muc_PARSnp/P_2018_05_10_103523990822
|-OS:           Linux
|-threads:      4
****************************************************************************************************************

<<Parsnp started>>

-->Reading Genome (asm, fasta) files from ./genomes/..
  |->[OK]
-->Reading Genbank file(s) for reference (.gbk) ..
  |->[WARNING]: no genbank file provided for reference annotations, skipping..
-->Running Parsnp multi-MUM search and libMUSCLE aligner..
**ERROR**
The following command failed:
>>/tmp/_MEIsm0xgl/parsnp /gpfs/gsfs4/users/Segrelab/Mucor2017/results/parsnp_genome/Muc_PARSnp/P_2018_05_10_103523990822/parsnpAligner.ini
Please veryify input data and restart Parsnp. If the problem persists please contact the Parsnp development team.
**ERROR**
10:35 cn3115 Muc_PARSnp$ uname -a
Linux cn3115 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

Any idea what is causing this???

[sconlan]

I think I'm getting different outputs from parsnp compiled for different operating systems. Unfortunately, I can't reproduce this error, because this issue is preventing me from running the OS X compiled version. The previously functional version is on a laptop I no longer have (but ran parsnp v 1.2).

[bkille]

There has been a major update to input parsing, so I'm not sure if this is still an error in the updated version. I can confirm that I can run commands w/ similar syntax, though.