Error while running DPPDIV on CIPRES

[Chloe Tan]

Hi,

When I ran the tool with a tree file with no branch length specified, I got this error message:

dppdiv-pthreads-avx: PLL/treeIO.c:954: treeReadLen: Assertion `0' failed.
/projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-DPPDIV-3E04D4C7DC68471BB7001E9F91171142/./_batch_command.cmdline: line 3:  1513 Aborted                 /projects/ps-ngbt/opt/comet/dppdiv2/pll-dppdiv-master/dppdiv-pthreads-avx -T 16 -in infile.txt -tre tree.tre -n 1000000 -pf 100 -sf 100 -out outfile -pm 3.0 -ra 2.0 -rb 4.0 -hsh 2.0 -s1 12345 -s2 12345
srun: error: comet-06-71: task 0: Exited with exit code 134

When I used one with branch lengths this is what it returned:

The file "tree.tre" has 0 lines. Could not find line 1
srun: error: comet-03-66: task 0: Exited with exit code 1

May I know what that means?

Thanks!

[Alexandros Stamatakis]

It looks as if this is a problem with the tree input file,

Alexis

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

[Chloe Tan]

Hi Alexis,

Since there's no manual available for the tool, at first I just used a rooted tree constructed from concatenated core gene alignment using IQ-TREE:

((((ATCC29927:0.00301571,(CITHA-6:3.23928e-005,GTA-HAF03:2.34323e-005)100:0.00305314)100:0.000768235,(FDAARGOS158:0.00306564,FDAARGOS230:0.0033078)96:0.00044009)100:0.0237255,((ATCC51873:0.0066108,bta3-1:0.00642111)100:0.00220528,HMSC23F03:0.00498143)100:0.013507):0.220394,((((NCTC8535:0.00549828,FDAARGOS350:0.00619122)100:0.001557,HUMV-5920:0.00676377)100:0.00189826,DSM30098:0.00702468)100:0.0167717,(((DSM30099:0.00919308,FB1:0.00958818)100:0.00300669,NCTC6578:0.0103538)100:0.00287284,(CBA7124:0.00399326,(ATCC13337:0.0044871,(ATCC29926:0.00411208,CBA7135:0.00436651)94:0.0010083)100:0.00104871)100:0.00711779)100:0.0159762):0.216529)100;

and got this error:

The file "tree.tre" has 0 lines. Could not find line 1
srun: error: comet-03-66: task 0: Exited with exit code 1

When I tried removing the branch lengths and bootstrap values:

((((ATCC29927,(CITHA-6,GTA-HAF03)),(FDAARGOS158,FDAARGOS230)),((ATCC51873,bta3-1),HMSC23F03)),((((NCTC8535,FDAARGOS350),HUMV-5920),DSM30098),(((DSM30099,FB1),NCTC6578),(CBA7124,(ATCC13337,(ATCC29926,CBA7135))))));

I got this:

dppdiv-pthreads-avx: PLL/treeIO.c:954: treeReadLen: Assertion `0' failed.
/projects/ps-ngbt/backend/

comet_workspace/NGBW-JOB-DPPDIV-3E04D4C7DC68471BB7001E9F91171142/./_batch_command.cmdline: line 3:  1513 Aborted                 /projects/ps-ngbt/opt/comet/dppdiv2/pll-dppdiv-master/dppdiv-pthreads-avx -T 16 -in infile.txt -tre tree.tre -n 1000000 -pf 100 -sf 100 -out outfile -pm 3.0 -ra 2.0 -rb 4.0 -hsh 2.0 -s1 12345 -s2 12345
srun: error: comet-06-71: task 0: Exited with exit code 134

Would you mind looking into my trees and let me know what's wrong with them?

Thank you so much!

Chloe

On Monday, 18 March 2019 16:21:47 UTC+8, alexandros.stamatakis wrote:

It looks as if this is a problem with the tree input file,

Alexis

On 18.03.19 07:30, Chloe Tan wrote:
> Hi,
>
> When I ran the tool with a tree file with no branch length specified, I
> got this error message:
>
> dppdiv-pthreads-avx: PLL/treeIO.c:954: treeReadLen: Assertion `0' failed.
> /projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-DPPDIV-3E04D4C7DC68471BB7001E9F91171142/./_batch_command.cmdline:
> line 3:  1513 Aborted                
> /projects/ps-ngbt/opt/comet/dppdiv2/pll-dppdiv-master/dppdiv-pthreads-avx -T
> 16 -in infile.txt -tre tree.tre -n 1000000 -pf 100 -sf 100 -out outfile
> -pm 3.0 -ra 2.0 -rb 4.0 -hsh 2.0 -s1 12345 -s2 12345
> srun: error: comet-06-71: task 0: Exited with exit code 134
>
>
> When I used one with branch lengths this is what it returned:
>
> The file "tree.tre" has 0 lines. Could not find line 1
> srun: error: comet-03-66: task 0: Exited with exit code 1
>
>
> May I know what that means?
>
>
> Thanks!
>
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> To unsubscribe from this group and stop receiving emails from it, send
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> <mailto:dppdiv-users+unsub...@googlegroups.com>.

[Tomas Flouri]

Hi Chloe,

try removing the inner node labels only and keep the branch lengths, i.e.

sed -i "s/)[0-9]\+/)/g" tree.txt

Tomas

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[Chloe Tan]

Hi Tomas,

I've tried that, this is what the tree looks like:

((((ATCC29927:0.00301571,(CITHA-6:3.23928E-5,GTA-HAF03:2.34323E-5):0.00305314):7.68235E-4,(FDAARGOS158:0.00306564,FDAARGOS230:0.0033078):4.4009E-4):0.0237255,((ATCC51873:0.0066108,bta3-1:0.00642111):0.00220528,HMSC23F03:0.00498143):0.013507):0.220394,((((NCTC8535:0.00549828,FDAARGOS350:0.00619122):0.001557,HUMV-5920:0.00676377):0.00189826,DSM30098:0.00702468):0.0167717,(((DSM30099:0.00919308,FB1:0.00958818):0.00300669,NCTC6578:0.0103538):0.00287284,(CBA7124:0.00399326,(ATCC13337:0.0044871,(ATCC29926:0.00411208,CBA7135:0.00436651):0.0010083):0.00104871):0.00711779):0.0159762):0.216529);

And this is what I got:

The file "tree.tre" has 0 lines. Could not find line 1
srun: error: comet-06-66: task 0: Exited with exit code 1

Chloe