Make sure program works

[Kalmasi2807]

Hello,

I'm running the program since last Thursday on 2 different servers. In once of them it shows me the progress print in the screen the results, in the other of them it doesn't print anything. I'm worried because I'm not sure if it works well.

I copy my commands (They are the same in 2 servers but different samples):

IntaRNA -t targets.fasta -q queries.fasta --threads=19 --seedBP=5 --energy=B --model=X --outMode=C --outCsvCols '*' --out=tMinE:minimal_energy_profiles.csv

Another problem is that in the server which prints the results it's the same results since last Sunday, it does not change.

How can I know if the program works well? I only can see the progress in the terminal with htop command and it runs but that's all.

Thanks so much

[martin-raden]

Hi @Kalmasi2807,

eventually it is hard to say what's going on in your system. Output might be delayed due to buffering (and delay depends on the buffer size and the problem specific output).

Generally speaking: computation can take a while, especially when you are running a big batch job with many sequences.

Since IntaRNA first computes accessibility information for ALL sequences, you wont see any output before that is done. So the more and longer sequences you have the longer this will take.

Since all accessibility data is hold in memory, you might exceed your RAM causing swapping of data to your hard drive, which slows down computation dramatically. (check with htop for swapping and memory consumption).

If you are interested in logging information, you can use the "-v"erbose output of IntaRNA (which you cannot enable after starting.. so no help for you two jobs).

Hope that helps. If so, please close the issue.

Best, Martin

[Kalmasi2807]

Hello @martin-raden,

I used -v command as you said me and I have this warning. ¿Is it about the RAM memory because it not has enough memory?

# INFO : Executed [IntaRNA::AccessibilityBasePair::AccessibilityBasePair(const IntaRNA::RnaSequence&, size_t, const IntaRNA::AccessibilityConstraint*, IntaRNA::E_type, IntaRNA::Z_type, size_t)] in [0 ms]
# VERBOSE : computing accessibility for query 'URS0000C5AD2A_109478'...
# VERBOSE : computing accessibility via Nussinov-like recursions...
# INFO : Executed [IntaRNA::AccessibilityBasePair::AccessibilityBasePair(const IntaRNA::RnaSequence&, size_t, const IntaRNA::AccessibilityConstraint*, IntaRNA::E_type, IntaRNA::Z_type, size_t)] in [1 ms]
# VERBOSE : computing accessibility for target 'NC_010443.5'...
# WARNING : Exception raised for :  #thread 0 #target 0 : std::bad_alloc
# WARNING : Exception raised : std::exception

[martin-raden]

Hi @Kalmasi2807

yes, most likely! "std::bad_alloc" errors are typically raised due to failed memory allocation attempts.

So eventually, this is not a "WARNING" as stated but an internal exception (causing the crash of thread 0) that will trigger IntaRNA to stop.

Hope that helps to investigate and counter the issue.

Best, Martin