h836472
commented
2 months ago Dear Sandro,
I will try to reproduce / diagnose the error but already think that it is the Diamond search step that fails with the error message: "Option is not permitted for this workflow: memory-limit". Need to look into this, but the error suggests that Diamond, with blastp search, does not support memory limitation. In the meantime, here are some options you might wish to try.
1., if you really need memory limitation, please try MMSeqs as the search tool (that was the configuration, we used on HPC nodes for multiple simultaneous CS runs with shared memory.) 2., start ContScout without specifying any memory limit option.
If you plan to run a single instance of ContScout on your server, you can safely omit the memory limit option. This option was included only for the special cases where multiple CS instances run simultaneously on the same machine sharing a common large (>786 GB) memory pool. There, by default, each instance would configure itself for the use all available RAM, causing clashes among the pipelines, Thus we manually set the memory limit that tells the aligner to proceed with smaller data chunks, ensuring that all CS instances nicely fit next to each other.
Balazs
On Sun, 28 Jul 2024 at 22:20, Sandro Valenzuela @.***> wrote:
Dear, along with greeting you, I am getting error related to the memory even though I have the resources.
error log:
Error: Option is not permitted for this workflow: memory-limit Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'Streptococcus_mitis_SK1080_tax_1008453_28Jul_2024_22_56/RefTaxLookup.ABC': No such file or directory Execution halted
stdout log:
This is ContScout, a contamination remover tool written in R.
Loading R libraries.
Temporary dir set to:/tmp. Pre-processing NCBI taxon database. Query taxon lineage: family:1300:Streptococcaceae order:186826:Lactobacillales class:91061:Bacilli phylum:1239:Bacillota kingdom:vk_1239:NA superkingdom:2:Bacteria
Analysis started at 2024-07-28 22:56:32 Command: -u /databases -d uniref100 -i query -q 1008453 -m 250G --pci 50 -c 2 -t /tmp -a diamond Databases used: Name: uniref100 Source: Uniprot NumProts: 398132654 DB_CRC: 210bc2cd Tax_CRC: a456430b MMSeqs_DB: uniref100/78df74ca/mmseqs/210bc2cd_uniref100_2024_02_tax.taxdb Diamond_DB: uniref100/78df74ca/diamond/210bc2cd_uniref100_2024_02_tax.taxdb.dmnd Creation_Date: 2024-04-28_23:53:17 Now reading fasta headers file. Now reading annotation file. Search command: diamond blastp -d /databases/uniref100/78df74ca/diamond/210bc2cd_uniref100_2024_02_tax.taxdb.dmnd -q protein_seq/1008453_Streptococcus_mitis.faa -o Streptococcus_mitis_SK1080_tax_1008453_28Jul_2024_22_56/RefTaxLookup.ABC --max-target-seqs 100 -f 6 qseqid sseqid bitscore qlen nident --threads 2 --memory-limit 250
command line:
singularity exec -B $new/software/ContScout:/databases -B $new/tmp:/tmp -B $(pwd)/query:/query $new/software/ContScout/contscout_latest.sif ContScout -u /databases -d uniref100 -i query -q $tid -m 250G --pci 50 -c 2 -t /tmp -a diamond
is it a memory issue?
thanks in advance, Sandro
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Sanrrone
Dear, along with greeting you, I am getting error related to the memory even though I have the resources.
error log:
stdout log:
command line:
is it a memory issue?
thanks in advance, Sandro