Kraken2 tool failing after SortMeRNA

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Hi there, I am looking for some help regarding one analysis in Kraken2 Tool. I am trying to run Kraken2 after filtering ribossomal RNA from my trimmed reads. My workflow goes like this: 1. Trim Galore, 2. SortMeRNa, 3. Kraken2 using the unaligned reads from the SortmeRNA outputs. However, when running Kraken2 keeps appearing an error and the job stops: Loading database information… done.
classify: malformed FASTQ file (exp. ‘@’, saw “AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEEEEEEEEEEAEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEAEEEAEE/EEEEEEAEEEEEEEEAEAEEEEAEAAAAEEEEEAEAAAEAAEEA<EAAEAAEEE”), aborting

Initially I thought that may be something happened since the beginning, so I did everything since step 0 (uploading raw reads, trimming, etc.) but did not work out.
Also, few days ago I try using Kraken2 with this same raw reads without using SortMeRNA tool, and it work out fine. That is why I am thinking that the problem may be in the SortMeRNA tool outputs. For note, I used the SortMeRNA tool for other raw reads of my reseach and it has been working out fine, no problems until now. I am leaving here the URL of my Galaxy history so you may be able to get into it and perhaps you notice something wrong that I am missing. Galaxy

Thank you very much in advance.
Janeth Ramirez.

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Hi @Janeth_Ramirez

Thanks for sharing the history, very helpful for this.

Yes, the reverse reads out of SortMeRNA were truncated. I reported this to the EU administrators to see if they can do anything about it server side. The tool probably needs more resources.

Meanwhile, try running fewer read pairs through this tool at a time to see if that helps. Check for intact fastq files with FastQC. Merge the reads that pass through back together before running Kraken. You could probably put all of this into a mini workflow to make this less tedious.

I did start a test here but the files might be too small to detect anything odd, and will definitely not trigger computation resources issues. This is mostly to double check that more is not going on. → https://usegalaxy.eu/u/jenj/h/test-sortmerna

Hope this helps! :slight_smile:

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Thanks for your help. I will try to do that workflow. Have a nice day.

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