-speciesList is not a valid option Error

[kim2039]

Hello,

I have some troubles, on Ubuntu 19.10

I tried to run "Mini example of annotating 2 genes in one query genome", however some issues about OpenSSL had occurred. (This problem had occurred on Ubuntu 17.10, too)

The issue seems to be from mafSpeciesSubset,

$ ~/Bioinformatics/tools/CESARTest/CESAR2.0/tools/mafSpeciesSubset

/home/kim/Bioinformatics/tools/CESARTest/CESAR2.0/tools/mafSpeciesSubset: /lib/x86_64-linux-gnu/libssl.so.10: version `libssl.so.10' not found (required by /home/kim/Bioinformatics/tools/CESARTest/CESAR2.0/tools/mafSpeciesSubset)
/home/kim/Bioinformatics/tools/CESARTest/CESAR2.0/tools/mafSpeciesSubset: /lib/x86_64-linux-gnu/libcrypto.so.10: version `libcrypto.so.10' not found (required by /home/kim/Bioinformatics/tools/CESARTest/CESAR2.0/tools/mafSpeciesSubset)

So, I downloaded latest UCSC tools and replaced. (Downloaded from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/)

The error about openSSL seems to be solved, but a new issue had occurred,

kim@kim-Ubuntu:~/Bioinformatics/tools/CESAR2.0/extra/miniExample$ annotateGenesViaCESAR.pl SNRNP25 hg38_oryAfe1.bb twoGenes.gp.forCESAR hg38 oryAfe1 CESARoutput 2bitDir $profilePath -maxMemory 1

Processing gene 'SNRNP25'
-specieslist is not a valid option
Error running '/bin/bash -c 'set -o pipefail; mafExtract -region=chr16:53989-54058 hg38_oryAfe1.bb stdout|echo stdin|mafSpeciesSubset stdin specieslist=oryAfe1,hg38 species.lst=NULL /dev/shm/exon.maf.C5j9jZxF0''

How do I solve this problem?

Thanks, Kim

[MichaelHiller]

Hi Kim,

I assume that you have installed the UCSC kent source code, which provides the original mafSpeciesSubset that does not have the -speciesList option. We added this in the code provided.

Pls run which mafSpeciesSubset to check if that refers to the binary in the tools/ directory.

If not, pls set export PATH=pwd/tools:$PATH such that the shell first looks into the tools dir.

Let me know if that does not work. Michael

[kim2039]

Hello, Michael,

I ran $ which mafSpeciesSubset and it worked and show /tools/mafSpeciesSubset binary file.

And both of original mafSpeciesSubset binary and your mafSpeciesSubset binary seem not to work, same error messages like below.

your binary

$ annotateGenesViaCESAR.pl SNRNP25 hg38_oryAfe1.bb twoGenes.gp.forCESAR hg38 oryAfe1 CESARoutput 2bitDir $profilePath -maxMemory 1

Processing gene 'SNRNP25'
mafSpeciesSubset: /lib/x86_64-linux-gnu/libssl.so.10: version `libssl.so.10' not found (required by mafSpeciesSubset)
mafSpeciesSubset: /lib/x86_64-linux-gnu/libcrypto.so.10: version `libcrypto.so.10' not found (required by mafSpeciesSubset)
Error running '/bin/bash -c 'set -o pipefail; mafExtract -region=chr16:53989-54058 hg38_oryAfe1.bb stdout|mafSpeciesSubset stdin NULL /dev/shm/exon.maf.SlBrW0N3l -speciesList=oryAfe1,hg38''

original latest binary

$ annotateGenesViaCESAR.pl SNRNP25 hg38_oryAfe1.bb twoGenes.gp.forCESAR hg38 oryAfe1 CESARoutput 2bitDir $profilePath -maxMemory 1

Processing gene 'SNRNP25'
-speciesList is not a valid option
Error running '/bin/bash -c 'set -o pipefail; mafExtract -region=chr16:53989-54058 hg38_oryAfe1.bb stdout|mafSpeciesSubset stdin NULL /dev/shm/exon.maf.bpAlrDf2M -speciesList=oryAfe1,hg38''

I tried to run original binary and made symbolic link to libssl.so.10 and libcrypto.so.10, but don't work because of difference of the version.

Thanks, Kim

[MichaelHiller]

Hi Kim,

the problem is that the provided mafSpeciesSubset does not work due to issues with the libraries.

I have now added a lightweight kent source with the source code of mafSpeciesSubset. Please clone CESAR2.0 again and follow the updated instructions.

It should work now. If not, pls let me know.

Thanks a lot Michael

[kim2039]

Hello Michael,

Thank you!! It works!

However, to run "Mini example", I had to replace some binary files (overlapSelect, bedSort, twoBitToFa) with latest version because of same errors,

`libssl.so.10' not found `libcrypto.so.10' not found

But other error didn't occur.

Thanks a lot, Kim