erro in step 10

[Panda-smile]

Hello professor, I generated the same error in step 10 during analysis (coassembly, Seqmerge). Is it caused by memory? (Cluster single node, memory = 480G, 64 threads)

seqmerge：

coassembly：

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10.mapsamples.txt SqueezeMeta_conf.txt coassembly.txt

Hello, Professor, could you please give me some guidance on how to modify the script in step 10 so that it can run individual samples one by one to reduce memory requirements?

1. I also try N=7, memory=240G，t=8，still erro. the overall configuration should be sufficient to handle this task since there are a total of 7×240=1680G of memory available.

   
   2. Running a single sample against the last recommendation, here are the corresponding results

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10.mapsamples.txt SqueezeMeta_conf.txt co assembly.txt

您好，教授，您能否指导我如何修改步骤 10 中的脚本，使其可以逐一运行各个样本以减少内存需求？

1. 我也尝试了N=7，内存=240G，t=8，还是报错。总体配置应该足以处理此任务，因为总共有 7×240=1680G 可用内存。
2. 针对最后的建议运行单个样本，以下是相应的结果

@fpusan hello professor~wish for your reply I am reaching out for your guidance and assistance with some technical challenges I have encountered during my metagenomics analysis project. Briefly, I am utilizing the SqueezeMeta software for analyzing metagenomics data. During the read mapping step, I unfortunately encountered an out-of-memory error, leading to an interruption in the analysis workflow. Despite allocating substantial resources for the SLURM job, the problem persists. The error message indicates a std::bad_alloc error, suggesting that the Bowtie2 mapping phase failed to allocate the required memory space.

[jtamames]

Hello It already works that way, mapping samples sequentially. It is indeed a memory problem. This looks like some configuration issue in your cluster preventing the use of more memory. You should ask your system admin to know if that is the case. Best, J

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你好， 它已经以这种方式工作，按顺序映射样本。确实是内存问题。这看起来像是集群中的某些配置问题导致无法使用更多内存。您应该询问您的系统管理员以了解情况是否如此。 贝斯特， J

thanks for professors reply，i will try ~is there any advice on parameters setting？ At the same time, I would like to ask the professor whether it is necessary to remove rRNA contamination when metatranscriptome is removed from the host? Will this affect the identification of EUK or 16s species?

[fpusan]

If I understand your question correctly, ideally you would remove rRNA contamination before sequencing. It is not the end of the world if you don't, but most of your reads will be coming from rRNA rather than mRNA. If using SQMtools to make plots, this will show as a large fraction of reads classified as "No CDS".

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well done~

[fpusan]

I will assume that this worked and close the issue, feel free to reopen otherwise