Help: Error with psicoffee

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He Song

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Jul 24, 2020, 4:49:52 AM7/24/20
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Dear all,

I am trying to align sequeces with psicoffee. I have the newest version of blast in the path, as well as local nr database: 'export BLASTDB=/home/hs/database/blastdb/'.  The blastp runs well: blastp -query 320.fasta -db nr

The t_coffee is installed as instructed and working well on other applications. However, I got error message when I using psicoffee.

t_coffee 320.fasta -mode psicoffee

PROGRAM: T-COFFEE Version_13.41.139.ca96b3d (2020-07-23 15:47:56 - Revision 7788a2c - Build 604)
-full_log      S [0] 
-genepred_score S [0] nsd
-run_name      S [0] 
-mem_mode      S [0] mem
-extend        D [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
-setenv        S [0] 0
-export        S [0] 0
-template_mode S [0] 
-flip          D [0]
-remove_template_file D [0]
-profile_template_file S [0] 
-in            S [1] Mproba_pair
-seq            S [1] 320.fasta
-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]
-filter_lib    D [0]
-shrink_lib    D [0]
-out_lib        W_F [0] no
-out_lib_mode  S [0] primary
-lib_only      D [0]
-outseqweight  W_F [0] no
-seq_source    S [0] ANY
-cosmetic_penalty D [0]
-gapopen        D [0]
-gapext        D [0]
-fgapopen      D [0]
-fgapext        D [0]
-nomatch        D [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]
-infile        R_F [0] 
-matrix        S [0] default
-tg_mode        D [0]
-profile_mode  S [0] cw_profile_profile
-profile_comparison S [0] profile
-dp_mode        S [0] linked_pair_wise
-ktuple        D [0]
-ndiag          D [0]
-diag_threshold D [0]
-diag_mode      D [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]
-ulimit        D [0] -1 
-maxnseq        D [0] -1 
-maxlen        D [0] -1 
-sample_dp      D [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]
-len            D [0]
-scale          D [0]
-mocca_interactive FL [0] 0
-method_evaluate_mode S [0] default
-color_mode    S [0] new
-aln_line_length D [0]
-evaluate_mode S [0] triplet
-get_type      FL [0] 0
-clean_aln      D [0]
-clean_threshold D [1]
-clean_iteration D [1]
-clean_evaluate_mode S [0] t_coffee_fast
-extend_matrix FL [0] 0
-prot_min_sim  D [0]
-prot_max_sim  D [100] 100 
-psiJ          D [0]
-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]
-lalign_n_top  D [0] 10 
-iterate        D [0]
-trim          D [0]
-split          D [0]
-trimfile      S [0] default
-split          D [0]
-split_nseq_thres D [0]
-split_score_thres D [0]
-check_pdb_status D [0]
-clean_seq_name D [0]
-seq_to_keep    S [0] 
-dpa_master_aln S [0] 
-dpa_maxnseq    D [0]
-dpa_min_score1 D [0] 
-dpa_min_score2 D [0] 
-dpa_keep_tmpfile FL [0] 0
-dpa_debug      D [0]
-multi_core    S [0] templates_jobs_relax_msa_evaluate
-n_core        D [0]
-thread        D [0]
-max_n_proc    D [0]
-lib_list      S [0] 
-prune_lib_mode S [0] 5
-tip            S [0] none
-rna_lib        S [0] 
-no_warning    D [0]
-run_local_script D [0]
-proxy          S [0] unset
-email          S [0] 
-clean_overaln D [0]
-overaln_param S [0] 
-overaln_mode  S [0] 
-overaln_model S [0] 
-overaln_threshold D [0]
-overaln_target D [0]
-overaln_P1    D [0]
-overaln_P2    D [0]
-overaln_P3    D [0]
-overaln_P4    D [0]
-exon_boundaries S [0] 
-display        D [0] 100 

INPUT FILES
Input File (M) proba_pair 
Input File (S) 320.fasta  Format fasta_seq

Identify Master Sequences [no]:

Master Sequences Identified
Looking For Sequence Templates:

Template Type: [BLAST] Mode Or File: [BLAST] [Start
3401 -- WARNING: Could Not Use EMAIL

pid 3375 -- Could not Run t_coffee -other_pg tc_generic_method.pl -mode=profile_template -database=uniref50 -method=blastp -cache=/home/hs/local/t_coffee//cache/ -minid=0 -maxid=100 -mincov=90 -trim=100 -server=EBI -type=_R_ -infile=/var/tmp/tco/tcotv7d_l2v3375//25627337578czr134 -outfile=320_prf1.template_list -tmpdir=/var/tmp/tco/tcotv7d_l2v3375/ to find templates[T-COFFEE](unforked mode) 
]
pid 3375 -- Impossible to find BLAST Templates Check that your blast server is properly installed [See documentation][FATAL:T-COFFEE] 

I also try to run psicoffee locally, however, similar error message appeared. Could you please help me to set it up correctly? Thanks. 

t_coffee 320.fasta -mode psicoffee -blast_server=LOCAL -protein_db=/home/hs/database/blastdb/nr

PROGRAM: T-COFFEE Version_13.41.139.ca96b3d (2020-07-23 15:47:56 - Revision 7788a2c - Build 604)
-full_log      S [0] 
-genepred_score S [0] nsd
-run_name      S [0] 
-mem_mode      S [0] mem
-extend        D [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
-setenv        S [0] 0
-export        S [0] 0
-template_mode S [0] 
-flip          D [0]
-remove_template_file D [0]
-profile_template_file S [0] 
-in            S [1] Mproba_pair
-seq            S [1] 320.fasta
-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]
-filter_lib    D [0]
-shrink_lib    D [0]
-out_lib        W_F [0] no
-out_lib_mode  S [0] primary
-lib_only      D [0]
-outseqweight  W_F [0] no
-seq_source    S [0] ANY
-cosmetic_penalty D [0]
-gapopen        D [0]
-gapext        D [0]
-fgapopen      D [0]
-fgapext        D [0]
-nomatch        D [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]
-infile        R_F [0] 
-matrix        S [0] default
-tg_mode        D [0]
-profile_mode  S [0] cw_profile_profile
-profile_comparison S [0] profile
-dp_mode        S [0] linked_pair_wise
-ktuple        D [0]
-ndiag          D [0]
-diag_threshold D [0]
-diag_mode      D [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]
-ulimit        D [0] -1 
-maxnseq        D [0] -1 
-maxlen        D [0] -1 
-sample_dp      D [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]
-len            D [0]
-scale          D [0]
-mocca_interactive FL [0] 0
-method_evaluate_mode S [0] default
-color_mode    S [0] new
-aln_line_length D [0]
-evaluate_mode S [0] triplet
-get_type      FL [0] 0
-clean_aln      D [0]
-clean_threshold D [1]
-clean_iteration D [1]
-clean_evaluate_mode S [0] t_coffee_fast
-extend_matrix FL [0] 0
-prot_min_sim  D [0]
-prot_max_sim  D [100] 100 
-psiJ          D [0]
-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 [1] LOCAL
-pdb_db        W_F [0] pdb
-protein_db    W_F [1] /home/hs/database/blastdb/nr
-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]
-lalign_n_top  D [0] 10 
-iterate        D [0]
-trim          D [0]
-split          D [0]
-trimfile      S [0] default
-split          D [0]
-split_nseq_thres D [0]
-split_score_thres D [0]
-check_pdb_status D [0]
-clean_seq_name D [0]
-seq_to_keep    S [0] 
-dpa_master_aln S [0] 
-dpa_maxnseq    D [0]
-dpa_min_score1 D [0] 
-dpa_min_score2 D [0] 
-dpa_keep_tmpfile FL [0] 0
-dpa_debug      D [0]
-multi_core    S [0] templates_jobs_relax_msa_evaluate
-n_core        D [0]
-thread        D [0]
-max_n_proc    D [0]
-lib_list      S [0] 
-prune_lib_mode S [0] 5
-tip            S [0] none
-rna_lib        S [0] 
-no_warning    D [0]
-run_local_script D [0]
-proxy          S [0] unset
-email          S [0] 
-clean_overaln D [0]
-overaln_param S [0] 
-overaln_mode  S [0] 
-overaln_model S [0] 
-overaln_threshold D [0]
-overaln_target D [0]
-overaln_P1    D [0]
-overaln_P2    D [0]
-overaln_P3    D [0]
-overaln_P4    D [0]
-exon_boundaries S [0] 
-display        D [0] 100 

INPUT FILES
Input File (M) proba_pair 
Input File (S) 320.fasta  Format fasta_seq

Identify Master Sequences [no]:

Master Sequences Identified
Precompute the Blasts -- Use Cache if available

--ERROR: Database /home/hs/database/blastdb/nr not available


*************************************************************************************************
*                        FULL TRACE BACK PID: 3590                                    
3590 -- ERROR: Database /home/hs/database/blastdb/nr not available
3590 -- COM: t_coffee 320.fasta -mode psicoffee -blast_server LOCAL -protein_db /home/hs/database/blastdb/nr 
3590 -- STACK: 3313 -> 3590
*************************************************************************************************

Best,
He

Cedric Notredame

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Jul 24, 2020, 5:07:08 AM7/24/20
to tco...@googlegroups.com, He Song

Hello,

I am not sure about the remote, as it may have to do with an issue accessing the EBI remote server, or the querry being too large.

We now recommend using LOCAL blast installations,

On this specific example, it means you must have the database /home/hs/database/blastdb/nr properly installed. THe link sghould be a link to the original file, not the directory

Cheers,


Cedric

Le 24/7/20 à 10:49, He Song a écrit :
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