Dears, I am trying to run t_coffe with -mode fmcoffee, but it is not using additional cores. Also I tried t_coffee -in in.fasta -mode fmcoffee -thread 4 -n_core 4 -cpu 4 -multi_core 4 -max_n_proc 4 -outfile out.fasta. None of this flags works for fmcoffee step (kalign, muscle).

is there other flag to use multithread in fmcoffee mode?.

thanks in advance, Sandro

Dear tcoffee developers :-)

I would like to align ~1000 with t-coffee and since the webserver is limited to 150 sequences, I wanted to try on my local computer (MAC OSX11-intel). I installed the beta version since I had issues with the stable one, and actually, I think the issue is similar. So I tested first on 10 sequences and this is the output:

✗  t_coffee test.fasta -mode=expresso [email protected]

PROGRAM: T-COFFEE Version_13.45.33.7d7e789 (Version_13.45.33.7d7e789)
-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] 	EXPRESSO
-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	[1] 	EXPRESSO
-in            	S	[0]
-seq           	S	[1] 	test.fasta
-aln           	S	[0]
-method_limits 	S	[0]
-method        	S	[1] 	sap_pair
-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	[1] 	[email protected]
-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.fasta  Format fasta_seq
	Input File (M) sap_pair

Identify Master Sequences [no]:

Master Sequences Identified
Looking For Sequence Templates:

	Template Type: [EXPRESSO] Mode Or File: [EXPRESSO] [Start
80366 -- WARNING: [ncbiblast_lwp.pl] [t_coffee -other_pg ncbiblast_lwp.pl --email [email protected] --database pdb --program blastp --outfile outfile --alignments 5 --stype protein seqfile>/dev/null 2>file.3070.32811428769.80366] failed to produce xml output -- will ne tried again [1]
80366 -- WARNING: [ncbiblast_lwp.pl] [t_coffee -other_pg ncbiblast_lwp.pl --email [email protected] --database pdb --program blastp --outfile outfile --alignments 5 --stype protein seqfile>/dev/null 2>file.3070.32811428769.80366] failed to produce xml output -- will ne tried again [2]
80366 -- WARNING: [ncbiblast_lwp.pl] [t_coffee -other_pg ncbiblast_lwp.pl --email [email protected] --database pdb --program blastp --outfile outfile --alignments 5 --stype protein seqfile>/dev/null 2>file.3070.32811428769.80366] failed to produce xml output -- will ne tried again [3]
80366 -- WARNING: [ncbiblast_lwp.pl] [t_coffee -other_pg ncbiblast_lwp.pl --email [email protected] --database pdb --program blastp --outfile outfile --alignments 5 --stype protein seqfile>/dev/null 2>file.3070.32811428769.80366] failed to produce xml output -- will ne tried again [4]
80366 -- WARNING: [ncbiblast_lwp.pl] [t_coffee -other_pg ncbiblast_lwp.pl --email [email protected] --database pdb --program blastp --outfile outfile --alignments 5 --stype protein seqfile>/dev/null 2>file.3070.32811428769.80366] failed to produce xml output
80366 -- WARNING: Blast for 1btkA00 failed (Run: 1 out of 2. Use NCBI)


*************************************************************************************************
*                        FULL TRACE BACK PID: 80361
80366 -- ERROR: BLAST_FAILURE::NCBI does not Support psiblast mode (-j3)
80366 -- COM: tc_generic_method.pl
80366 -- STACK: 80361 -> 80366
*************************************************************************************************


*************************************************************************************************
*                        MESSAGES RECAPITULATION
80366 -- WARNING: [ncbiblast_lwp.pl] [t_coffee -other_pg ncbiblast_lwp.pl --email [email protected] --database pdb --program blastp --outfile outfile --alignments 5 --stype protein seqfile>/dev/null 2>file.3070.32811428769.80366] failed to produce xml output -- will ne tried again [1]
80366 -- WARNING: [ncbiblast_lwp.pl] [t_coffee -other_pg ncbiblast_lwp.pl --email [email protected] --database pdb --program blastp --outfile outfile --alignments 5 --stype protein seqfile>/dev/null 2>file.3070.32811428769.80366] failed to produce xml output -- will ne tried again [2]
80366 -- WARNING: [ncbiblast_lwp.pl] [t_coffee -other_pg ncbiblast_lwp.pl --email [email protected] --database pdb --program blastp --outfile outfile --alignments 5 --stype protein seqfile>/dev/null 2>file.3070.32811428769.80366] failed to produce xml output -- will ne tried again [3]
80366 -- WARNING: [ncbiblast_lwp.pl] [t_coffee -other_pg ncbiblast_lwp.pl --email [email protected] --database pdb --program blastp --outfile outfile --alignments 5 --stype protein seqfile>/dev/null 2>file.3070.32811428769.80366] failed to produce xml output -- will ne tried again [4]
80366 -- WARNING: [ncbiblast_lwp.pl] [t_coffee -other_pg ncbiblast_lwp.pl --email [email protected] --database pdb --program blastp --outfile outfile --alignments 5 --stype protein seqfile>/dev/null 2>file.3070.32811428769.80366] failed to produce xml output
80366 -- WARNING: Blast for 1btkA00 failed (Run: 1 out of 2. Use NCBI)
*************************************************************************************************

# TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 80361 ppid 80346
#CL: /var/tmp/tco/tcokytpn68r80346/9752780346th1ii1.pl -other_pg tc_generic_method.pl -mode=pdb_template -database=pdb -method=blastp -cache=/Users/thibault/.t_coffee/cache/ -minid=35 -maxid=100 -mincov=50 -server=EBI -type=_P_ -pdb_type=d -infile=/var/tmp/tco/tcokytpn68r80346/9752780346th1ii134 -outfile=test_pdb1.template_list -tmpdir=/var/tmp/tco/tcokytpn68r80346/


*************************************************************************************************
*                        FULL TRACE BACK PID: 80346
80361 -- ERROR: UNSPECIFIED UNSPECIFIED
80361 -- COM: /var/tmp/tco/tcokytpn68r80346/9752780346th1ii1.pl -other_pg tc_generic_method.pl -mode=pdb_template -database=pdb -method=blastp -cache=/Users/thibault/.t_coffee/cache/ -minid=35 -maxid=100 -mincov=50 -server=EBI -type=_P_ -pdb_type=d -infile=/var/tmp/tco/tcokytpn68r80346/9752780346th1ii134 -outfile=test_pdb1.template_list -tmpdir=/var/tmp/tco/tcokytpn68r80346/
80361 -- STACK: 80346 -> 80361
*************************************************************************************************

# TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 80346 ppid 73380
#CL: t_coffee test.fasta -mode expresso -email [email protected]

Do you know how can I fix this :-) ?

Best regards, Thibault.

I manage to use t_coffee on a fasta with 3 sequences but then I tried with a set of 80 then 200 and both times nothing happens. I tried : t_coffee myseqs.faa and it gets stuck at : "--- Process Method/Library/Aln Mproba_pair"

t_coffee -quicktree -reg -seq myseqs.faa gets stuck at "!Compute Guide Tree --- "

t_coffee -version PROGRAM: T-COFFEE Version_13.41.0.28bdc39 (2019-11-30 10:21:53 - Revision 5d5a1c1 - Build 465)

--ERROR: MAX_N_PID exceded -- Recompile changing the value of MAX_N_PID (current: 260000 Requested: 280441)

Hi,

I was looking into the bug #917143 inside Debian and tried to reproduce it with the source that you provide from your home page. The failing command is:

./t_coffee -aln=../example/sproteases_small.muscle,../example/sproteases_small.tc_aln,../example/sproteases_small.b62_aln -outfile=combined-aln.aln

Here is the stderr of the command: tcoffee.stderr.log

It seems that there is a bug, but I find it difficult to start tracking it down based on the error message. Interestingly, that with two (not three) input alignments it doesn't fail.

EDITED: t_coffee.ErrorReport file doesn't get generated for some reason.

Building tcoffee-11.00.8cbe486 on OS X 10.8 with Xcode5.1 (clang compiler) and gcc5 (via fink) for other compilers gives me a bunch of -Wempty-body warnings. They are for code such as:

dp_lib/evaluate.c:1946:13: warning: if statement has empty body [-Wempty-body]
      if (w);free_int (w, -1);
            ^
dp_lib/evaluate.c:1946:13: note: put the semicolon on a separate line to silence this warning

It's seeing the first semicolon as the end of the whole if/then, not the end of the "if" clause (that feels like a bash syntax?), which would mean free_int is not in the "then" block. A total of 8 such warnings scattered. Let me know if this is indeed a correct detection of a mistake and I'll pull out the rest from by build logs.

If t_coffee is installed in a directory where the path contains a space and the fully qualified path is passed on the command line as such:

/Applications/Genetic\ Software/t_coffee -infile TCoffeeInput15_Mar_04_15_23_30_1 -outfile TCoffeeOutput15_Mar_04_15_23_30_2 -newtree TCoffeeInput15_Mar_04_15_23_30_1.dnd -output fasta_aln -type PROTEIN -dp_mode myers_miller_pair_wise

t_coffee fails internally to handle the space in argv[0] with the following error:

--ERROR: : Software/t_coffee does not exist [FATAL] ************************************************************************************************* * FULL TRACE BACK PID: 68544
68544 -- ERROR: : Software/t_coffee does not exist [FATAL]

Greetings,

In the context of the debian project, we noticed that t_coffee version 13.45.0.4846264 is causing a test failure in biopython 1.79. It turns out that the following command:

$ t_coffee \
        -output clustalw_aln \
        -infile Fasta/fa01 \
        -outfile Fasta/tc_out.aln \
        -type protein \
        -outorder input \
        -gapopen -2 \
        -gapext -5

is causing a segmentation fault when run with the following ./Fasta/fa01 input file:

>AK1H_ECOLI/1-378
CPDSINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDPVEKLLAVG-HYLESTVDIAE
STRRIAASRIP------A-DHMVLMAGFTAGN-EKGELVVLGRNGSDYSAAVLAACLRAD
CCEIWTDVNGVYTCDP-------------RQVPDARLLKSMSYQEAMELSY--FGAKVLH
PRTITPIAQFQIPCLIKNTGNPQAPGTL-IG--ASRDEDELP----VKGISNLN------
NMAMFSVSGP-GMKGMVGMAARVFAAMS-------RARISVVLITQSSSEYSISFCVPQS
DCVRAERAMLEEFY-----LELKEGLLEPLAVAERLAIISV-VGDGLRTLRGISAKF---
---FAALARANINIVAIA
>AKH_HAEIN/1-382
-----------------VEDAVKATIDCRGEKLSIAMMKAWFEARGY-S--VHIVDPVKQ
LLAKG-GYLESSVEIEESTKRVDAANIA--K-DKVVLMAGF---TAGNEKGELVLLGRNG
SDYSAAC-----------------LAACLGASVCEIWTDVDGVYTCDP--RLVPDARLLP
TLSYREAMELSYFGAKVIHPRTIGPLLPQNIPCVIKNTGNPSAPGSI-ID--GNVKSESL
Q----VKGITNLDNLAMFNVSGPGMQGM---VGMASRVFSAMSGAGISVILITQSSSEYS
---ISFCVPVKSAEVAKTVLETEFA-----NELNEHQLEPIEVIKDLSIISV-VGDGMKQ
AKGIAARF------FSALAQAN

Here is a backtrace of the affected portion; the intercepted sequence pointer S is NULL, which is probably the root of the segmentation fault:

#0  0x0000555555675e73 in seq2unique_name_seq (S=0x0) at util_lib/aln_convertion_util.c:2091
#1  0x000055555574d656 in read_seq_in_n_list (fname=0x55555598cad0, n=1, type=0x55555593dfb0 "", SeqMode=0x555555d45fb0 "ANY") at util_lib/util_constraints_list.c:2533
#2  0x0000555555659491 in batch_main (argc=15, argv=0x555555944230) at t_coffee_lib/t_coffee.c:4720
#3  0x000055555564f9a0 in main (argc=15, argv=0x7fffffffe128) at t_coffee_lib/t_coffee.c:179

You can lookup Debian Bug#1022570 for some further details, but I tried to gather the most relevant information here.

Have a nice day, :) Étienne.

just wasted a couple of hours because I had previously installed T-COFFEE and it had edited a bunch of startup files behind my back to add export PERL5LIB=

Can you please not do this?? There are other ways to set paths for a given program without modifying the behavior other, unrelated programs.

First of all, thank you very much for your work and dedication, I really enjoy using the t_coffee suite.

I am running a multiple alignment of a fasta containing ~7500 sequences with these lengths:

file     format  type     num_seqs    sum_len  min_len  avg_len  max_len
1_1.faa  FASTA   Protein     7,582  7,901,142      300  1,042.1   13,093

These are the commands that I'm using:

t_coffee -other_pg seq_reformat -in 1_1.faa -output code_name > 1_1.code_name
t_coffee -other_pg seq_reformat -code 1_1.code_name -in 1_1.faa > 1_1.coded.fasta
t_coffee -reg -seq 1_1.coded.fasta -nseq 750 -tree mbed -method maffteinsi_msa -outfile 1_1.coded.aln -outtree 1_1.coded.mbed -thread 20
t_coffee -other_pg seq_reformat -decode 1_1.code_name -in 1_1.coded.aln > 1_1.aln

At a certain point, the output remains in this state

In addition, t_coffee remains in process state S (interruptable sleep) consuming ~60GB of RAM. After several days of checking the process, it does not seem to move from there. I have tried restarting the alignment several times but it keeps stopping at the same point.

Do I have to leave it until it finishes?

Is it possible to estimate how long it may take? I have aligned other files with slightly smaller sizes a little below and I have not had this kind of problem. Could it be due to the large size difference (from 300aa to >13 000aa) ?

The max pid is incorrectly set. In previous issues there is a suggestion that max pid can be set as an environment variable, but there is no documentation of what this variable should be anywhere nor what version of t_coffee supports this behavior. When t_coffee complains about the max pid it says to set the variable and recompile, but again there is no indication of how to achieve this. How can we properly set the max pid?