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Thanks for reporting this issue. Do you mind providing me with gtdb16Sexport_VS78.txt, so I can reproduce? Mail to [email protected], if it's small enough and you are okay with sharing it. Or you can attach it to this issue on github. Thanks,
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
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