Problems in assembly and taxonomic assignment
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11 weeks ago

Hello everyone, I hope you are very well. I'm having trouble getting assembly parsing done for me either using MEGAHIT OR METASPADE in OMICSBOX. Also, without going through a previous assembly, these are not analyzed by krakren. The analysis advances more or less up to 66% (both methods), then it generates an error.

Let's talk a bit about my samples. These were obtained from a highly polluted lake in Mexico. We analyze them by NOVASEQ 6000 PE 150 bp technology. Therefore, I have 4 files per sample, since that sequencer has two flow cells (61_L001_R1, 61_L001_R2 61_L002_R1 y 61_L002_R2). So, I have two R1s, and two R2s from a single sample. I did not make any merge (join) of the R1s, nor of the R2s. Do you consider it necessary to do so? If so, could you tell me how? Thanks in advance. CAT FUNCTION DIDN'T WORK

So, the 30 samples (120 in total = 30x4), I previously analyzed them by fastqpreprocessing, and then I did the quality check. Everything went well up to those two steps. Then, I wanted to do the assembly or the taxonomic classification, but I got an error. It is important to mention that I also analyzed the raw samples (without preprocessing), because I no longer knew what else the error could be. I attach only one sample (4 files).

I hope you can help me solve what is happening. I would appreciate it infinitely. https://drive.google.com/drive/folders/1f_uYxZT-6cwH8rb5GLHbeiQGWsca6la8?usp=sharing

novaseq6000 PES1 assembly omicsbox illumina • 183 views
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Dear Osiris, Omicsbox is a commercial application, if I am not mistaken. Therefore, your first contact should be their customer support, https://www.biobam.com/contact-us/ giving a more precise error message. Customer support is part of what they get paid for, also it is almost impossible for us to help without access to the software and code, in fact the company already should have all the necessary data in their logs to debug your problem.

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