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Stuck at 100% - tcoffee regressive mode #48

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pentamorfico opened this issue Nov 25, 2021 · 0 comments
Open

Stuck at 100% - tcoffee regressive mode #48

pentamorfico opened this issue Nov 25, 2021 · 0 comments

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@pentamorfico
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pentamorfico commented Nov 25, 2021

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

imagen

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) ?

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