Hi everyone,
I encountered an issue while running CSAtool. This is my command and report:
What’s free(): invalid next size (fast)? Maybe it’s due to the way I formatted the sequences?
I hope you can help me.
Thanks!
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marco.barr •
It looks like you're running some sort of heavy analysis from an HPC login node. Login nodes are not meant for resource (RAM/CPU/time) intensive work and your sysadmin might have set limits on how much resource can be consumed in a single login. Use compute nodes to run your analysis.
I started the same analysis in parallel in sbatch slurm by setting 1 compute node, 64 RAM and 10 CPU threads but I get the same error. How many nodes should I use since I'm at the maximum usable limit for RAM and CPU for the cluster?
Is this the tool you're using: https://github.com/fjdf/CSA ?
Yes this is it. There is nothing written about this on the manual page
I simplified the path in the screenshot because it was too long but I put all the correct path... Furthermore, when I run ./CSA -h it suggests me not to put R after CSA to obtain both rotation, alignment and plot. Maybe I try to put R?
Have you checked the example files provided https://github.com/fjdf/CSA/blob/master/website/Examples.zip?raw=true and made sure your program runs properly? I just checked and had no issue running the tool with examples (which seem to be simple multi-line fasta files).
You are right in that CSA can be run in many ways depending on what you are trying to do.
$ ./CSA
[ Multiple Circular Sequence Aligner v1.11 ]
> USAGE:
[ Rotate+Align+Image ] ./CSA <multi-fasta-file>
[ Rotation only ] ./CSA R <multi-fasta-file>
[ Alignment only ] ./CSA A <multi-fasta-file>
[Alignment Image only] ./CSA I <multi-fasta-file>
> TOOLS:
[ Clean FASTA file ] ./CSA C <multi-fasta-file>
[Get Alignment Score ] ./CSA S <multi-fasta-file>
[Convert FASTA to MSF] ./CSA M <multi-fasta-file>
You can also make sure your fasta is clean by using
./CSA C Multi_fasta.txt
I had already tried with the examples to initially familiarize myself with the tool and everything worked. Now I'll try to clean my fasta and give you updates
Hi Genomax, I'm trying to clean the fasta sequence and the output is:
[ Multiple Circular Sequence Aligner v1.11 ] Loading sequences from file </home/Multi_fasta.txt> ... (179338 bytes) ERROR: Can't write output file
Subsequently I tried to run Alignment Image only and results:
barresi.m@login01:~/Nanoporei/CSA$ ./CSA I /home/Multi_fasta.txt [ Multiple Circular Sequence Aligner v1.11 ] > ERROR: Consensus sizes don't match
what could I try to do? Is reformatting the file so that the size of the reference matches my reads? Thanks for your help.
I also wrote to the developers of the tool
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marco.barr •
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