Alignment file read failed with error code 3

[tv195]

Hi,
I am running SSU align without any problems:
ssu-align --dna gtdb16Sexport_VS78.txt ssu_aligned_VS78

But then I get this error, when running the command:
ssu-mask --afa ssu_aligned_VS78

ssu-mask :: mask SSU rRNA alignments

SSU-ALIGN 0.1 (June 2010)

Copyright (C) 2010 HHMI Janelia Farm Research Campus

Freely distributed under the GNU General Public License (GPLv3)

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

command: ssu-mask --afa ssu_aligned_VS78

date: Thu Mar 30 15:24:41 2017

Masking alignments based on posterior probabilities...

mask

------------

file name in/out type #cols incl. excl.

---------------------------------- ------ ---- ----- ----- -----

ssu_aligned_VS78.archaea.stk input aln 11832 - -
ssu_aligned_VS78.archaea.mask output mask 1508 1386 122
ssu_aligned_VS78.archaea.mask.pdf output pdf 1508 1386 122
ssu_aligned_VS78.archaea.mask.afa output aln 1386 - -

FATAL: Failed command: ssu-esl-alimask --rna --small -p --pfract 0.95 --pthresh 0.95 --fmask-rf ssu_aligned_VS78/ssu_aligned_VS78.bacteria.mask -o ssu_aligned_VS78/ssu_aligned_VS78.bacteria.mask.stk ssu_aligned_VS78/ssu_aligned_VS78.bacteria.stk > ssu_aligned_VS78.bacteria.alimask 2> ssu_aligned_VS78/ssutmp8erraa93990
Output (STDOUT):NONE
Output (STDERR):
Alignment file read failed with error code 3
P~

Would be great to know what error code 3 means.
Also it ran fine on another data set on the same server, so the installation works.
Cheers,
Chris

[nawrockie]

Hi Chris,

Thanks for reporting this issue. Do you mind providing me with gtdb16Sexport_VS78.txt, so I can reproduce? Mail to nawrocke@ncbi.nlm.nih.gov, if it's small enough and you are okay with sharing it. Or you can attach it to this issue on github. Thanks,

Eric