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cbcrg / tcoffee

A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
http://tcoffee.org
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t_coffee Needed by T-COFFEE Could not be found #66

Closed alephreish closed 3 months ago

alephreish commented 3 months ago 
$ t_coffee -version
PROGRAM: T-COFFEE Version_13.46.0.919e8c6b (2023-07-07 22:06:42 - Revision 29996c5 - Build 980)

I cannot make t_coffee run psicoffee. See a minimal example below. Also, not sure if it uses blast+ or legacy blast - which one should I use to create a local database?

$ cat test.fas 
>1
MAYWLQAASLLVLLALSPGADAAAAQHLCGSHLVDALYLVCGEKGFFYNPKRDLLYCFWFLSPKSAKENEEYPFKDQMEMMVKRGIVEQCCHKPCNIFDLQNYCN
>2
MALWMRLLPLLALLALWEPNPAQAFVNQHLCGSHLVEALYLVCGERGFFYTPKSRRGVEDPQVTQLELGGGPGAGDLQTLALEVAQQKRGIVDQCCTSICSLYQLENYCN
>3
MALWIRSLPLLALLALSGPGTSQAAANQHLCGSHLVEALYLVCGERGFFYSPKARRDVERPLVSSPLHGEVGELPFQQEEFEKVKRGIVEQCCHNTCSLYQLENYCN
$ t_coffee test.fas -mode=psicoffee

#*****************************************************************
--ERROR: #  [FATAL:T-COFFEE]

# The Program /opt/t_coffee/bin/t_coffee Needed by T-COFFEE Could not be found
# If /opt/t_coffee/bin/t_coffee is installed on your system:
#        -Make sure /opt/t_coffee/bin/t_coffee is in your $path:
# If /opt/t_coffee/bin/t_coffee is NOT installed obtain a copy from:
#   (null)
#
#
# and install it manualy
******************************************************************

*************************************************************************************************
*                        FULL TRACE BACK PID: 1602385                                    
1602385 -- ERROR: #  [FATAL:T-COFFEE]
1602385 -- COM: /opt/t_coffee/bin/t_coffee test.fas -mode psicoffee 
1602385 -- STACK: 1602384 -> 1602385
*************************************************************************************************

# TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 1602385 ppid 1602384
#CL: /opt/t_coffee/bin/t_coffee test.fas -mode psicoffee 
$ t_coffee test.fas -method=psicoffee_msa

PROGRAM: T-COFFEE Version_13.46.0.919e8c6b (2023-07-07 22:06:42 - Revision 29996c5 - Build 980)
-full_log       S   [0] 
-genepred_score S   [0]     nsd
-run_name       S   [0] 
-mem_mode       S   [0]     mem
-extend         D   [1]     1 
-extend_mode    S   [0]     very_fast_triplet
-max_n_pair     D   [0]     10 
-seq_name_for_quadruplet    S   [0]     all
-compact        S   [0]     default
-clean          S   [0]     no
-do_self        FL  [0]     0
-do_normalise   D   [0]     1000 
-template_file  S   [0] 
-template_dir_E_    S   [0]     ./
-setenv         S   [0]     0
-export         S   [0]     0
-template_mode  S   [0] 
-flip           D   [0]     0 
-remove_template_file   D   [0]     0 
-profile_template_file  S   [0] 
-in             S   [0] 
-seq            S   [1]     test.fas
-aln            S   [0] 
-method_limits  S   [0] 
-method         S   [1]     psicoffee_msa
-lib            S   [0] 
-profile        S   [0] 
-profile1       S   [0] 
-profile2       S   [0] 
-pdb            S   [0] 
-relax_lib      D   [0]     1 
-filter_lib     D   [0]     0 
-shrink_lib     D   [0]     0 
-out_lib        W_F [0]     no
-out_lib_mode   S   [0]     primary
-lib_only       D   [0]     0 
-outseqweight   W_F [0]     no
-seq_source     S   [0]     ANY
-cosmetic_penalty   D   [0]     0 
-gapopen        D   [0]     0 
-gapext         D   [0]     0 
-fgapopen       D   [0]     0 
-fgapext        D   [0]     0 
-nomatch        D   [0]     0 
-newtree        W_F [0]     default
-tree           W_F [0]     NO
-usetree        R_F [0] 
-tree_mode      S   [0]     nj
-distance_matrix_mode   S   [0]     ktup
-distance_matrix_sim_mode   S   [0]     idmat_sim1
-quicktree      FL  [0]     0
-outfile        W_F [0]     default
-maximise       FL  [1]     1
-output         S   [0]     aln html
-len            D   [0]     0 
-infile         R_F [0] 
-matrix         S   [0]     default
-fs_matrix      S   [0]     idmat
-fs_gop         D   [0]     1 
-fs_gep         D   [0]     1 
-tg_mode        D   [0]     1 
-profile_mode   S   [0]     cw_profile_profile
-profile_comparison S   [0]     profile
-dp_mode        S   [0]     linked_pair_wise
-ktuple         D   [0]     1 
-ndiag          D   [0]     0 
-diag_threshold D   [0]     0 
-diag_mode      D   [0]     0 
-sim_matrix     S   [0]     vasiliky
-transform      S   [0] 
-extend_seq     FL  [0]     0
-outorder       S   [0]     input
-inorder        S   [0]     aligned
-seqnos         S   [0]     off
-case           S   [0]     keep
-cpu            D   [0]     0 
-ulimit         D   [0]     -1 
-maxnseq        D   [0]     -1 
-maxlen         D   [0]     -1 
-sample_dp      D   [0]     0 
-weight         S   [0]     default
-seq_weight     S   [0]     no
-align          FL  [1]     1
-mocca          FL  [0]     0
-domain         FL  [0]     0
-start          D   [0]     0 
-len            D   [0]     0 
-scale          D   [0]     0 
-mocca_interactive  FL  [0]     0
-method_evaluate_mode   S   [0]     default
-color_mode     S   [0]     new
-aln_line_length    D   [0]     0 
-evaluate_mode  S   [0]     triplet
-get_type       FL  [0]     0
-clean_aln      D   [0]     0 
-clean_threshold    D   [1]     1 
-clean_iteration    D   [1]     1 
-clean_evaluate_mode    S   [0]     t_coffee_fast
-extend_matrix  FL  [0]     0
-prot_min_sim   D   [0]     0 
-prot_max_sim   D   [100]   100 
-psiJ           D   [0]     3 
-psitrim_mode   S   [0]     regtrim
-psitrim_tree   S   [0]     codnd
-psitrim        D   [100]   100 
-prot_min_cov   D   [90]    90 
-pdb_type       S   [0]     d
-pdb_min_sim    D   [35]    35 
-pdb_max_sim    D   [100]   100 
-pdb_min_cov    D   [50]    50 
-pdb_blast_server   W_F [0]     EBI
-blast          W_F [0] 
-blast_server   W_F [0]     EBI
-pdb_db         W_F [0]     pdb
-protein_db     W_F [0]     uniref50
-method_log     W_F [0]     no
-struc_to_use   S   [0] 
-cache          W_F [0]     use
-print_cache    FL  [0]     0
-align_pdb_param_file   W_F [0]     no
-align_pdb_hasch_mode   W_F [0]     hasch_ca_trace_bubble
-external_aligner   S   [0]     NO
-msa_mode       S   [0]     tree
-et_mode        S   [0]     et
-master         S   [0]     no
-blast_nseq     D   [0]     0 
-lalign_n_top   D   [0]     10 
-iterate        D   [0]     0 
-trim           D   [0]     0 
-split          D   [0]     0 
-trimfile       S   [0]     default
-split          D   [0]     0 
-split_nseq_thres   D   [0]     0 
-split_score_thres  D   [0]     0 
-check_pdb_status   D   [0]     0 
-clean_seq_name D   [0]     0 
-seq_to_keep    S   [0] 
-dpa_master_aln S   [0] 
-dpa_maxnseq    D   [0]     0 
-dpa_min_score1 D   [0] 
-dpa_min_score2 D   [0] 
-dpa_keep_tmpfile   FL  [0]     0
-dpa_debug      D   [0]     0 
-multi_core     S   [0]     templates_jobs_relax_msa_evaluate
-n_core         D   [0]     1 
-thread         D   [0]     1 
-max_n_proc     D   [0]     1 
-lib_list       S   [0] 
-prune_lib_mode S   [0]     5
-tip            S   [0]     none
-rna_lib        S   [0] 
-no_warning     D   [0]     0 
-run_local_script   D   [0]     0 
-proxy          S   [0]     unset
-email          S   [0] 
-clean_overaln  D   [0]     0 
-overaln_param  S   [0] 
-overaln_mode   S   [0] 
-overaln_model  S   [0] 
-overaln_threshold  D   [0]     0 
-overaln_target D   [0]     0 
-overaln_P1     D   [0]     0 
-overaln_P2     D   [0]     0 
-overaln_P3     D   [0]     0 
-overaln_P4     D   [0]     0 
-exon_boundaries    S   [0] 
-display        D   [0]     100 

INPUT FILES
    Input File (S) test.fas  Format fasta_seq
    Input File (M) psicoffee_msa 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 3 SEQUENCES  [PROTEIN]
  Input File test.fas Seq 1 Length  105 type PROTEIN Struct Unchecked
  Input File test.fas Seq 2 Length  110 type PROTEIN Struct Unchecked
  Input File test.fas Seq 3 Length  107 type PROTEIN Struct Unchecked

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

    --- Process Method/Library/Aln Stest.fas
    xxx Retrieved Stest.fas
    --- Process Method/Library/Aln Mpsicoffee_msa
pid 1602719 -- COMMAND FAILED: dynamic.pl  -seq /var/tmp/tco/tco7ybgty2j1602712//73061602718t9uia272  -outfile /var/tmp/tco/tco7ybgty2j1602712//73061602718t9uia271        -method psicoffee_msa   >>/dev/null 2>&1

    xxx Retrieved Mpsicoffee_msa

    All Methods Retrieved

****************** ERROR *****************************************

You have not provided any method or enough Sequences[FATAL]
If you have used the '-in' Flag, ADD the methods you wish to use:
    -in <your sequences> Mlalign_id_pair Mfast_pair

And make sure you provide at least TWO sequences
/opt/t_coffee/bin/t_coffee -seq test.fas -method psicoffee_msa 
*****************************************************************

*************************************************************************************************
*                        MESSAGES RECAPITULATION                                    
1602719 -- WARNING: COMMAND FAILED: dynamic.pl  -seq /var/tmp/tco/tco7ybgty2j1602712//73061602718t9uia272  -outfile /var/tmp/tco/tco7ybgty2j1602712//73061602718t9uia271        -method psicoffee_msa   >>/dev/null 2>&1
*************************************************************************************************
cnotred commented 3 months ago

Hello Andrey

The problem seems to be that T-coffee is not on your PATH. In this specific mode T-Coffee calls itself.

From what I see in your output, having t_coffee in

/opt/t_coffee/bin/

Should do the trick

You should use legacy blast

Cheers

Cedric

--

Dr Cedric Notredame, PhD ORCID - https://orcid.org/0000-0003-1461-0988https://urldefense.com/v3/__https://orcid.org/0000-0003-1461-0988__;!!D9dNQwwGXtA!SMc4j2BjfVrbtIkNLgH9GMyKYaeMTwLyLZOY3ekmpRVksWfqAb3vYibX4HPTOmrkgdLvI8sL7E0LUiwBHJhlxDvKNUIvshE$

On 17 Jul 2024, at 13:55, Andrey Rozenberg @.***> wrote:



$ t_coffee -version PROGRAM: T-COFFEE Version_13.46.0.919e8c6b (2023-07-07 22:06:42 - Revision 29996c5 - Build 980)

I cannot make t_coffee run psicoffee. See a minimal example below. Also, not sure if it uses blast+ or legacy blast - which one should I use to create a local database?

$ cat test.fas

1 MAYWLQAASLLVLLALSPGADAAAAQHLCGSHLVDALYLVCGEKGFFYNPKRDLLYCFWFLSPKSAKENEEYPFKDQMEMMVKRGIVEQCCHKPCNIFDLQNYCN 2 MALWMRLLPLLALLALWEPNPAQAFVNQHLCGSHLVEALYLVCGERGFFYTPKSRRGVEDPQVTQLELGGGPGAGDLQTLALEVAQQKRGIVDQCCTSICSLYQLENYCN 3 MALWIRSLPLLALLALSGPGTSQAAANQHLCGSHLVEALYLVCGERGFFYSPKARRDVERPLVSSPLHGEVGELPFQQEEFEKVKRGIVEQCCHNTCSLYQLENYCN $ t_coffee test.fas -mode=psicoffee

*****

--ERROR: # [FATAL:T-COFFEE]

The Program /opt/t_coffee/bin/t_coffee Needed by T-COFFEE Could not be found

If /opt/t_coffee/bin/t_coffee is installed on your system:

-Make sure /opt/t_coffee/bin/t_coffee is in your $path:

If /opt/t_coffee/bin/t_coffee is NOT installed obtain a copy from:

(null)

# #

and install it manualy

TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 1602385 ppid 1602384

CL: /opt/t_coffee/bin/t_coffee test.fas -mode psicoffee

$ t_coffee test.fas -method=psicoffee_msa

PROGRAM: T-COFFEE Version_13.46.0.919e8c6b (2023-07-07 22:06:42 - Revision 29996c5 - Build 980) -full_log S [0] -genepred_score S [0] nsd -run_name S [0] -mem_mode S [0] mem -extend D [1] 1 -extend_mode S [0] very_fast_triplet -max_n_pair D [0] 10 -seq_name_for_quadruplet S [0] all -compact S [0] default -clean S [0] no -do_self FL [0] 0 -do_normalise D [0] 1000 -template_file S [0] -template_dirE S [0] ./ -setenv S [0] 0 -export S [0] 0 -template_mode S [0] -flip D [0] 0 -remove_template_file D [0] 0 -profile_template_file S [0] -in S [0] -seq S [1] test.fas -aln S [0] -method_limits S [0] -method S [1] psicoffee_msa -lib S [0] -profile S [0] -profile1 S [0] -profile2 S [0] -pdb S [0] -relax_lib D [0] 1 -filter_lib D [0] 0 -shrink_lib D [0] 0 -out_lib W_F [0] no -out_lib_mode S [0] primary -lib_only D [0] 0 -outseqweight W_F [0] no -seq_source S [0] ANY -cosmetic_penalty D [0] 0 -gapopen D [0] 0 -gapext D [0] 0 -fgapopen D [0] 0 -fgapext D [0] 0 -nomatch D [0] 0 -newtree W_F [0] default -tree W_F [0] NO -usetree R_F [0] -tree_mode S [0] nj -distance_matrix_mode S [0] ktup -distance_matrix_sim_mode S [0] idmat_sim1 -quicktree FL [0] 0 -outfile W_F [0] default -maximise FL [1] 1 -output S [0] aln html -len D [0] 0 -infile R_F [0] -matrix S [0] default -fs_matrix S [0] idmat -fs_gop D [0] 1 -fs_gep D [0] 1 -tg_mode D [0] 1 -profile_mode S [0] cw_profile_profile -profile_comparison S [0] profile -dp_mode S [0] linked_pair_wise -ktuple D [0] 1 -ndiag D [0] 0 -diag_threshold D [0] 0 -diag_mode D [0] 0 -sim_matrix S [0] vasiliky -transform S [0] -extend_seq FL [0] 0 -outorder S [0] input -inorder S [0] aligned -seqnos S [0] off -case S [0] keep -cpu D [0] 0 -ulimit D [0] -1 -maxnseq D [0] -1 -maxlen D [0] -1 -sample_dp D [0] 0 -weight S [0] default -seq_weight S [0] no -align FL [1] 1 -mocca FL [0] 0 -domain FL [0] 0 -start D [0] 0 -len D [0] 0 -scale D [0] 0 -mocca_interactive FL [0] 0 -method_evaluate_mode S [0] default -color_mode S [0] new -aln_line_length D [0] 0 -evaluate_mode S [0] triplet -get_type FL [0] 0 -clean_aln D [0] 0 -clean_threshold D [1] 1 -clean_iteration D [1] 1 -clean_evaluate_mode S [0] t_coffee_fast -extend_matrix FL [0] 0 -prot_min_sim D [0] 0 -prot_max_sim D [100] 100 -psiJ D [0] 3 -psitrim_mode S [0] regtrim -psitrim_tree S [0] codnd -psitrim D [100] 100 -prot_min_cov D [90] 90 -pdb_type S [0] d -pdb_min_sim D [35] 35 -pdb_max_sim D [100] 100 -pdb_min_cov D [50] 50 -pdb_blast_server W_F [0] EBI -blast W_F [0] -blast_server W_F [0] EBI -pdb_db W_F [0] pdb -protein_db W_F [0] uniref50 -method_log W_F [0] no -struc_to_use S [0] -cache W_F [0] use -print_cache FL [0] 0 -align_pdb_param_file W_F [0] no -align_pdb_hasch_mode W_F [0] hasch_ca_trace_bubble -external_aligner S [0] NO -msa_mode S [0] tree -et_mode S [0] et -master S [0] no -blast_nseq D [0] 0 -lalign_n_top D [0] 10 -iterate D [0] 0 -trim D [0] 0 -split D [0] 0 -trimfile S [0] default -split D [0] 0 -split_nseq_thres D [0] 0 -split_score_thres D [0] 0 -check_pdb_status D [0] 0 -clean_seq_name D [0] 0 -seq_to_keep S [0] -dpa_master_aln S [0] -dpa_maxnseq D [0] 0 -dpa_min_score1 D [0] -dpa_min_score2 D [0] -dpa_keep_tmpfile FL [0] 0 -dpa_debug D [0] 0 -multi_core S [0] templates_jobs_relax_msa_evaluate -n_core D [0] 1 -thread D [0] 1 -max_n_proc D [0] 1 -lib_list S [0] -prune_lib_mode S [0] 5 -tip S [0] none -rna_lib S [0] -no_warning D [0] 0 -run_local_script D [0] 0 -proxy S [0] unset -email S [0] -clean_overaln D [0] 0 -overaln_param S [0] -overaln_mode S [0] -overaln_model S [0] -overaln_threshold D [0] 0 -overaln_target D [0] 0 -overaln_P1 D [0] 0 -overaln_P2 D [0] 0 -overaln_P3 D [0] 0 -overaln_P4 D [0] 0 -exon_boundaries S [0] -display D [0] 100

INPUT FILES Input File (S) test.fas Format fasta_seq Input File (M) psicoffee_msa

Identify Master Sequences [no]:

Master Sequences Identified INPUT SEQUENCES: 3 SEQUENCES [PROTEIN] Input File test.fas Seq 1 Length 105 type PROTEIN Struct Unchecked Input File test.fas Seq 2 Length 110 type PROTEIN Struct Unchecked Input File test.fas Seq 3 Length 107 type PROTEIN Struct Unchecked

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

    --- Process Method/Library/Aln Stest.fas
    xxx Retrieved Stest.fas
    --- Process Method/Library/Aln Mpsicoffee_msa

pid 1602719 -- COMMAND FAILED: dynamic.pl -seq /var/tmp/tco/tco7ybgty2j1602712//73061602718t9uia272 -outfile /var/tmp/tco/tco7ybgty2j1602712//73061602718t9uia271 -method psicoffee_msa >>/dev/null 2>&1

    xxx Retrieved Mpsicoffee_msa

    All Methods Retrieved

** ERROR *****

You have not provided any method or enough Sequences[FATAL] If you have used the '-in' Flag, ADD the methods you wish to use: -in Mlalign_id_pair Mfast_pair

And make sure you provide at least TWO sequences /opt/t_coffee/bin/t_coffee -seq test.fas -method psicoffee_msa

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alephreish commented 3 months ago

That's the problem, it is there and I added the path to the $PATH:

$ ls -lh /opt/t_coffee/bin/t_coffee
-rwxr-xr-x 1 root root 3.0M Jul  8  2023 /opt/t_coffee/bin/t_coffee
$ echo $PATH
/loads_of_other_paths:/opt/t_coffee/bin
$ MAX_N_PID_4_TCOFFEE=100000000 /opt/t_coffee/bin/t_coffee test.fas -mode=psicoffee

#*****************************************************************
--ERROR: #  [FATAL:T-COFFEE]

# The Program /opt/t_coffee/bin/t_coffee Needed by T-COFFEE Could not be found
# If /opt/t_coffee/bin/t_coffee is installed on your system:
#        -Make sure /opt/t_coffee/bin/t_coffee is in your $path:
# If /opt/t_coffee/bin/t_coffee is NOT installed obtain a copy from:
#   (null)
#
#
# and install it manualy
******************************************************************

*************************************************************************************************
*                        FULL TRACE BACK PID: 1615165                                    
1615165 -- ERROR: #  [FATAL:T-COFFEE]
1615165 -- COM: /opt/t_coffee/bin/t_coffee test.fas -mode psicoffee 
1615165 -- STACK: 1502629 -> 1615165
*************************************************************************************************

# TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 1615165 ppid 1502629
#CL: /opt/t_coffee/bin/t_coffee test.fas -mode psicoffee

I was originally trying to run it with conda facing the same issues but currently debugging it with the system-wide installation.

cnotred commented 3 months ago

This is strange. Could it be other t_coffee versions around? What if you type ‘which t_coffee’ from a new shell

--

Dr Cedric Notredame, PhD ORCID - https://orcid.org/0000-0003-1461-0988https://urldefense.com/v3/__https://orcid.org/0000-0003-1461-0988__;!!D9dNQwwGXtA!SMc4j2BjfVrbtIkNLgH9GMyKYaeMTwLyLZOY3ekmpRVksWfqAb3vYibX4HPTOmrkgdLvI8sL7E0LUiwBHJhlxDvKNUIvshE$

On 17 Jul 2024, at 14:21, Andrey Rozenberg @.***> wrote:



That's the problem, it is there and I added the path to the $PATH:

$ ls -lh /opt/t_coffee/bin/t_coffee -rwxr-xr-x 1 root root 3.0M Jul 8 2023 /opt/t_coffee/bin/t_coffee $ echo $PATH /loads_of_other_paths:/opt/t_coffee/bin $ MAX_N_PID_4_TCOFFEE=100000000 /opt/t_coffee/bin/t_coffee test.fas -mode=psicoffee

*****

--ERROR: # [FATAL:T-COFFEE]

The Program /opt/t_coffee/bin/t_coffee Needed by T-COFFEE Could not be found

If /opt/t_coffee/bin/t_coffee is installed on your system:

-Make sure /opt/t_coffee/bin/t_coffee is in your $path:

If /opt/t_coffee/bin/t_coffee is NOT installed obtain a copy from:

(null)

# #

and install it manualy

TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 1615165 ppid 1502629

CL: /opt/t_coffee/bin/t_coffee test.fas -mode psicoffee

I was originally trying to run it with conda facing the same issues but currently debugging it with the system-wide installation.

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alephreish commented 3 months ago 
$ which t_coffee 
/usr/local/bin/t_coffee
$ cat /usr/local/bin/t_coffee
dir=/opt/t_coffee
MAX_N_PID_4_TCOFFEE=4194304 PLUGINS_4_TCOFFEE="$dir/plugins/linux" "$dir/bin/t_coffee" "$@"
$ ls -lh /opt/t_coffee
total 4.2M
drwxr-xr-x  3 root root 4.0K Jul 17 15:34 bin
drwxr-xr-x  2 root root 4.0K Jul 17 15:34 lck
drwxrwxrwx  2 root root 4.0K Jul 17 15:34 mcoffee
drwxrwxrwx  2 root root 4.0K Jul 17 15:34 methods
drwxr-xr-x  5 root root 4.0K Jul 17 15:34 perl
drwxrwxrwx  3 root root 4.0K Jul 17 15:34 plugins
drwxr-xr-x 10 root root 4.0K Jul 17 15:34 src
drwxr-xr-x  2 root root 4.0K Jul 17 15:34 tmp
-rwx------  1 root root 4.1M Jul 17 15:34 uninstall
-rw-r--r--  1 root root  11K Jul 17 15:34 uninstall.dat
$ ls -lh /opt/t_coffee/bin/
total 3.0M
drwxr-xr-x 2 root root 4.0K Jul 17 15:34 linux
-rwxr-xr-x 1 root root 3.0M Jul  8  2023 t_coffee

From a conda environment the error is the same:

#*****************************************************************
--ERROR: #  [FATAL:T-COFFEE]

# The Program /path_to_conda_env/libexec/t-coffee-13.46.0.919e8c6b-0/bin/linux/t_coffee Needed by T-COFFEE Could not be found
# If /path_to_conda_env/libexec/t-coffee-13.46.0.919e8c6b-0/bin/linux/t_coffee is installed on your system:
#        -Make sure /path_to_conda_env/libexec/t-coffee-13.46.0.919e8c6b-0/bin/linux/t_coffee is in your $path:
# If /path_to_conda_env/libexec/t-coffee-13.46.0.919e8c6b-0/bin/linux/t_coffee is NOT installed obtain a copy from:
#   (null)
#
#
# and install it manualy
******************************************************************

*************************************************************************************************
*                        FULL TRACE BACK PID: 1623734                                    
1623734 -- ERROR: #  [FATAL:T-COFFEE]
1623734 -- COM: /path_to_conda_env/libexec/t-coffee-13.46.0.919e8c6b-0/bin/linux/t_coffee test.fas -mode psicoffee 
1623734 -- STACK: 1623730 -> 1623734
*************************************************************************************************

# TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 1623734 ppid 1623730
#CL: /path_to_conda_env/libexec/t-coffee-13.46.0.919e8c6b-0/bin/linux/t_coffee test.fas -mode psicoffee
alephreish commented 3 months ago

Interesting, on a different linux machine with v. 13.39.0.d675aed installed in user's /home it does seem to work.

cnotred commented 3 months ago

Thanks Andrey. This looks like some kind of install issue. Do you have anyway to make a fresh install ? We will try to reproduce the issue on our side.

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On 17 Jul 2024, at 14:43, Andrey Rozenberg @.***> wrote:



Interesting, on a different linux machine with v. 13.39.0.d675aed installed in user's /home it does seem to work.

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alephreish commented 3 months ago

Yeah, Cedric it does seem to be related to installation. I've tried now to install v. 13.46 in three different ways:

On the second server I was in fact already having 13.46. I've checked that the differences between the three installation strategies are reproducible on both servers.

I'm ready to help with further debugging.

JoseEspinosa commented 3 months ago

Thanks for the feedback @alephreish! 😄 I made a test in a Linux machine where t_coffee has never been installed before:

  1. Using the installer here In this case after sourcing the updated .bashrc I get rid of the error.

  2. Directly from the tarball here In this case, I added t_coffee to my path and it worked:

    
./T-COFFEE_installer_Version_13.46.0.919e8c6b_linux_x64/bin/t_coffee test.fas -mode psicoffee

*****

--ERROR: # [FATAL:T-COFFEE]

The Program ./T-COFFEE_installer_Version_13.46.0.919e8c6b_linux_x64/bin/t_coffee Needed by T-COFFEE Could not be found

If ./T-COFFEE_installer_Version_13.46.0.919e8c6b_linux_x64/bin/t_coffee is installed on your system:

-Make sure ./T-COFFEE_installer_Version_13.46.0.919e8c6b_linux_x64/bin/t_coffee is in your $path:

If ./T-COFFEE_installer_Version_13.46.0.919e8c6b_linux_x64/bin/t_coffee is NOT installed obtain a copy from:

(null)

# #

and install it manualy

TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 18187 ppid 18084

Actually is not in my path yet

$ which t_coffee

I added to it

$ export PATH="/home/jespinosa/DELETE_ME/tcoffee_i_66/T-COFFEE_installer_Version_13.46.0.919e8c6b_linux_x64/bin:$PATH" (base) jespinosa@pardal:tcoffee_i_66$ which t_coffee /home/jespinosa/DELETE_ME/tcoffee_i_66/T-COFFEE_installer_Version_13.46.0.919e8c6b_linux_x64/bin/t_coffee

And then it worked

$ t_coffee test.fas -mode psicoffee

PROGRAM: T-COFFEE Version_13.46.0.919e8c6b (2023-07-07 22:06:42 - Revision 29996c5 - Build 980) -full_log S [0] -genepred_score S [0] nsd -run_name S [0] -mem_mode S [0] mem -extend D [1] 1 -extend_mode S [0] very_fast_triplet -max_n_pair D [0] 10 -seq_name_for_quadruplet S [0] all -compact S [0] default -clean S [0] no -do_self FL [0] 0 -do_normalise D [0] 1000 -template_file S [1] BLAST -template_dirE S [0] ./ -setenv S [0] 0 -export S [0] 0 -template_mode S [0] -flip D [0] 0 -remove_template_file D [0] 0 -profile_template_file S [0] -in S [1] Mproba_pair -seq S [1] test.fas -aln S [0] -method_limits S [0] -method S [0] -lib S [0] -profile S [0] -profile1 S [0] -profile2 S [0] -pdb S [0] -relax_lib D [0] 1 -filter_lib D [0] 0 -shrink_lib D [0] 0 -out_lib W_F [0] no -out_lib_mode S [0] primary -lib_only D [0] 0 -outseqweight W_F [0] no -seq_source S [0] ANY -cosmetic_penalty D [0] 0 -gapopen D [0] 0 -gapext D [0] 0 -fgapopen D [0] 0 -fgapext D [0] 0 -nomatch D [0] 0 -newtree W_F [0] default -tree W_F [0] NO -usetree R_F [0] -tree_mode S [0] nj -distance_matrix_mode S [0] ktup -distance_matrix_sim_mode S [0] idmat_sim1 -quicktree FL [0] 0 -outfile W_F [0] default -maximise FL [1] 1 -output S [0] aln html -len D [0] 0 -infile R_F [0] -matrix S [0] default -fs_matrix S [0] idmat -fs_gop D [0] 1 -fs_gep D [0] 1 -tg_mode D [0] 1 -profile_mode S [0] cw_profile_profile -profile_comparison S [0] profile -dp_mode S [0] linked_pair_wise -ktuple D [0] 1 -ndiag D [0] 0 -diag_threshold D [0] 0 -diag_mode D [0] 0 -sim_matrix S [0] vasiliky -transform S [0] -extend_seq FL [0] 0 -outorder S [0] input -inorder S [0] aligned -seqnos S [0] off -case S [0] keep -cpu D [0] 0 -ulimit D [0] -1 -maxnseq D [0] -1 -maxlen D [0] -1 -sample_dp D [0] 0 -weight S [0] default -seq_weight S [0] no -align FL [1] 1 -mocca FL [0] 0 -domain FL [0] 0 -start D [0] 0 -len D [0] 0 -scale D [0] 0 -mocca_interactive FL [0] 0 -method_evaluate_mode S [0] default -color_mode S [0] new -aln_line_length D [0] 0 -evaluate_mode S [0] triplet -get_type FL [0] 0 -clean_aln D [0] 0 -clean_threshold D [1] 1 -clean_iteration D [1] 1 -clean_evaluate_mode S [0] t_coffee_fast -extend_matrix FL [0] 0 -prot_min_sim D [0] 0 -prot_max_sim D [100] 100 -psiJ D [0] 3 -psitrim_mode S [0] regtrim -psitrim_tree S [0] codnd -psitrim D [100] 100 -prot_min_cov D [90] 90 -pdb_type S [0] d -pdb_min_sim D [35] 35 -pdb_max_sim D [100] 100 -pdb_min_cov D [50] 50 -pdb_blast_server W_F [0] EBI -blast W_F [0] -blast_server W_F [0] EBI -pdb_db W_F [0] pdb -protein_db W_F [0] uniref50 -method_log W_F [0] no -struc_to_use S [0] -cache W_F [0] use -print_cache FL [0] 0 -align_pdb_param_file W_F [0] no -align_pdb_hasch_mode W_F [0] hasch_ca_trace_bubble -external_aligner S [0] NO -msa_mode S [0] tree -et_mode S [0] et -master S [0] no -blast_nseq D [0] 0 -lalign_n_top D [0] 10 -iterate D [0] 0 -trim D [0] 0 -split D [0] 0 -trimfile S [0] default -split D [0] 0 -split_nseq_thres D [0] 0 -split_score_thres D [0] 0 -check_pdb_status D [0] 0 -clean_seq_name D [0] 0 -seq_to_keep S [0] -dpa_master_aln S [0] -dpa_maxnseq D [0] 0 -dpa_min_score1 D [0] -dpa_min_score2 D [0] -dpa_keep_tmpfile FL [0] 0 -dpa_debug D [0] 0 -multi_core S [0] templates_jobs_relax_msa_evaluate -n_core D [0] 1 -thread D [0] 1 -max_n_proc D [0] 1 -lib_list S [0] -prune_lib_mode S [0] 5 -tip S [0] none -rna_lib S [0] -no_warning D [0] 0 -run_local_script D [0] 0 -proxy S [0] unset -email S [0] -clean_overaln D [0] 0 -overaln_param S [0] -overaln_mode S [0] -overaln_model S [0] -overaln_threshold D [0] 0 -overaln_target D [0] 0 -overaln_P1 D [0] 0 -overaln_P2 D [0] 0 -overaln_P3 D [0] 0 -overaln_P4 D [0] 0 -exon_boundaries S [0] -display D [0] 100

INPUT FILES Input File (M) proba_pair Input File (S) test.fas Format fasta_seq

Identify Master Sequences [no]:

Master Sequences Identified Looking For Sequence Templates:

Template Type: [BLAST] Mode Or File: [BLAST] [Start

18227 -- WARNING: Could Not Use EMAIL

pid 18201 -- Could not Run t_coffee -other_pg tc_generic_method.pl -mode=profile_template -database=uniref50 -method=blastp -cache=/home/jespinosa/.t_coffee//cache/ -minid=0 -maxid=100 -mincov=90 -trim=100 -server=EBI -type=R -infile=/var/tmp/tco/tcovn5mqt6q18201//1783118201t517o136 -outfile=test_prf1.template_list -tmpdir=/var/tmp/tco/tcovn5mqt6q18201/ to find templates[T-COFFEE](unforked mode) ] pid 18201 -- Impossible to find BLAST Templates Check that your blast server is properly installed [See documentation][FATAL:T-COFFEE]

So as @cnotred mentioned, you may have a conflicting installation.

alephreish commented 3 months ago

Hi @JoseEspinosa, no, it's not due to conflicting installation.

It's due to environmental variables:

$ conda activate t_coffee_env
(t_coffee_env) $ env | grep COFFEE
# nothing

For the system-wide installation the environmental variables have to be fixed manually. For the conda-based installation I'd call this a bug. A workaround for conda:

export DIR_4_TCOFFEE=($CONDA_PREFIX/libexec/t-coffee-*)
export PERL5LIB=($CONDA_PREFIX/lib/5.*)
export PLUGINS_4_TCOFFEE=$DIR_4_TCOFFEE/plugins/linux
export PATH=$DIR_4_TCOFFEE/bin/linux:$PATH
export MAX_N_PID_4_TCOFFEE=4194304
alephreish commented 3 months ago

I'm closing this as installation in /home is the default for t_coffee, so anyone installing it system-wide should read the readme better and take care of the system variables themselves. The issue with the conda should be addressed in bioconda.

JoseEspinosa commented 3 months ago

I'm closing this as installation in /home is the default for t_coffee, so anyone installing it system-wide should read the readme better and take care of the system variables themselves. The issue with the conda should be addressed in bioconda.

OK, thanks for reporting!