Syntax Errors with ANGSD-wrapper

[ChaochihL]

There were multiple syntax errors that prevented the ANGSD-wrapper from running. One of the errors was in the inbreeding coefficients script which wasn't able to run. Since many of the wrappers depend on having an inbreeding coefficient, I was not able to test most of the scripts.

Syntax Errors

Here is a quick overview of the issues:

Attempt to run inbreeding coefficients script

Error message 1

/home/morrellp/liux1299/Arun/angsd-wrapper/scripts/utils.sh: line 13: syntax error in conditional expression

• fixed by adding a space before second pair of square brackets

Error message 2

/home/morrellp/liux1299/Arun/angsd-wrapper/scripts/utils.sh: line 35: syntax error in conditional expression

• fixed by adding a space before second pair of square brackets

Error message 3

./scripts/F.sh: line 29: syntax error in conditional expression: unexpected token `;'

• fixed by adding space

Error message 4

./scripts/F.sh: line 93: syntax error: unexpected end of file

• Was not able to fix this

  Attempt to run PCA script

Error message 1

./scripts/PCA.sh: line 25: syntax error in conditional expression: unexpected token `;' 

• Fixed error by adding space before second pair of square brackets

Error message 2

./scripts/PCA.sh: line 68: syntax error: unexpected end of file 

• Was not able to fix this

  Attempt to work through tutorial

• Error message 1 Command used:

cd angsd; make

Tail end of error output:

g++ -O3 -D_USE_KNETFILE  -o angsd *.o -lz -lpthread
g++ -O3 -D_USE_KNETFILE  -o angsd.static *.o -lz -lpthread --static
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
make: *** [angsd.static] Error 1

• The wording of what users should input for Reference and Ancestral genome sequence needs to be clarified
• FASTA.conf file needs to have comments
• common.conf file: REF_SEQ and ANC_SEQ should not be commented out. The tutorial should mention these can be edited in common.conf. OVERRIDE and REGIONS variables are left blank without anything assigned to them; the input users should place in those to spots is not mentioned in the tutorial.
• Use of sbatch should be explained in more detail because it is not available to everyone.
• After fixing the errors I could, I attempted to run ANGSD-wrapper with the following commands:

bash scripts/SFS.sh scripts/SFS.conf

And got the following error message

scripts/SFS.sh: line 130: syntax error: unexpected end of file

At this point I was not able to fix this error.

[arundurvasula]

Thanks for the great catches Chaochih! It looks like the unexpected end of file came from a block of if-else statements that were copied and pasted and but not syntax checked. I pushed an update to fix all the files where this occurred.

I added an explanation to the tutorial about sbatch and uncommented ANC and REF and added comments to FASTA.conf

[rossibarra]

The failed make is I think a zlib problem we've seen before in the UMN cluster isn't it? On Tue, 27 Oct 2015 at 08:50, Arun Durvasula notifications@github.com wrote:

Thanks for the great catches Chaochih! It looks like the unexpected end of file came from a block of if-else statements that were copied and pasted and but not syntax checked. I pushed an update to fix all the files where this occurred.

I added an explanation to the tutorial about sbatch and uncommented ANC and REF and added comments to FASTA.conf

— Reply to this email directly or view it on GitHub https://github.com/arundurvasula/angsd-wrapper/pull/98#issuecomment-151547514 .

[mojaveazure]

Yep.

[tvkent]

had the zlib problem on my server here, too