Help: Error with psicoffee
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He Song
Jul 24, 2020, 4:49:52 AM7/24/20
to Tcoffee
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] 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] 0
-remove_template_file D [0] 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] 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
-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) 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] 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] 0
-remove_template_file D [0] 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] 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
-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 [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] 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) 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
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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