pdb_pair/TMalign failed error

[Charlotte Crauwels]

Hello with the following command:

t_coffee -in=input.fasta -method=TMalign_pair,sap_pair -mode=3dcoffee 

       with the PDB_DIR variable set

       with in the file ~/t_coffee/cache/pdb_entry_type.txt: one line per pdb file: <pdb file/name sequence> prot crystal

I obtain the following output along with the alignment:

Multi Core Mode (read): 1 processor(s):

--- Process Method/Library/Aln Msap_pair
xxx Retrieved Msap_pair
--- Process Method/Library/Aln S/scratch/brussel/106/vsc10611/TCOFFEE/GPCRs_A/try.fasta
xxx Retrieved S/scratch/brussel/106/vsc10611/TCOFFEE/GPCRs_A/try.fasta
--- Process Method/Library/Aln Msap_pair
xxx Retrieved Msap_pair
--- Process Method/Library/Aln MTMalign_pair
pdb_pair/TMalign failed:
@»x

pdb_pair/TMalign failed:
@»x

pdb_pair/TMalign failed:
@»x

xxx Retrieved MTMalign_pair

All Methods Retrieved

does this mean the TMalign method didn't work? do you know what this error means?

Thank you for your help.

Kind regards,

Charlotte

[baltzis.a...@gmail.com]

Hi Charlotte,

Yes, exactly. Either TMalign is not properly installed in your system or it's a newer version (2022/4/12). If the latter is the case, could you try to install TMalign Version 20190822?

Best,

Athanasios

[Charlotte Crauwels]

Dear Athanasios,

Thank you for your answer, unfortunately,  with the TMalign Version 20190822 I get the same error. Nevertheless, I know TMalign is properly install as I can use it to align 2 structures. Any other idea how I could run 3D coffee with the following commands ?

module load TM-align/20190822-GCC-11.3.0
module load T-Coffee/13.45.61.3c310a9
module load SAP/1.1.3-GCC-11.3.0

SEQUENCE=/scratch/brussel/106/vsc10611/TCOFFEE/GPCRs_A/test.fasta
PDB=/scratch/brussel/106/vsc10611/TCOFFEE/GPCRs_A/PDB_DIR/

export PDB_DIR=$PDB

t_coffee -in=$SEQUENCE -method=TMalign_pair -mode=3dcoffee

with in ~/.t_coffee/cache/pdb_entry_type.txt:

Q96LB1 prot crystal
Q9NS66 prot crystal
P08908 prot crystal

I would really like to reproduce the results you obtain in your latest paper: https://doi.org/10.1093/bioinformatics/btac625 (so using 3D coffee with sap_pair and TMalign_pair)

Best,

Charlotte

[Athanasios Baltzis]

Dear Charlotte,

Have you tried to copy the pdb and fasta files to your working directory instead of using env variables, such as PDB_DIR, and then run:

t_coffee -in "yourfasta" -mode=3dcoffee  -template_file "your_template_file"

Moreover, if you want to reproduce our analysis with our data or with your own data, you can use our nextflow pipeline (as long as you have docker or singularity available in your system) https://github.com/cbcrg/msa-af2-nf, which takes care of all these issues related to the computing environments.

Best,

Athanasios 

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