Error - "COULD NOT Append anything" to tmp

[Anne Farrell]

I have been using TCoffee for protein alignments since August with no problems until yesterday. I have been trying to align 50 ribosomal protein files, with about ~123 sequences in each file. All the files do contain some missing sequence data with "?????" strings as placeholders. TCoffee has successfully aligned 41 of these files, but fails with the following error for nine of them. 

Error:

COULD NOT Append anything to /var/tmp/tco/tcounk4n6ra65041//253436504615456

I have confirmed that I have write and read permissions to the var/tmp/tco directory (ie suggested in this thread).

I tried reducing the number of cores by setting n_core based on a suggestion in this thread.

I tried cleaning the temp directory.

I am running:

Centos 7 (although I tried on Centos 6 as well)

Linux 3.10.0-693.21.1.el7.x86_64

T_coffee version 11

Command: t_coffee -in [file] -output fasta_aln

BUT!  If I just run the command on the file over and over, it will sometimes eventually work. I did manage to align three of nine by simply trying again and again.

I have sequence files and output to share if needed.

Thanks!

[Anne Farrell]

I just tried this thread's suggestions on changing my lck and tmp folders.  So far it seems to be working.  At least I'm no longer getting the "COULD NOT Append..." error.

[Cedric Notredame]

Dear Annie 

Getting rid of your ~/.t_coffee should also do the trick.

Thanks for using T-Coffee!

Cédric 

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Dr Cedric Notredame
Group Leader
Notredame's lab - Comparative Bioinformatics Group
Bioinformatics and Genomics Programme
Room 440.03

Centre de Regulació Genòmica (CRG)
Dr. Aiguader, 88
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Spain

Ph#     + 34 93 316 02 71
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email   cedric.n...@crg.eu
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ORC-ID: 0000-0003-1461-0988
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