Trimmomatic error; encountered a tool detected error

Hello
Im running Trimmomatic Pair-end(separate data set) with multiple data sets. Every data was fine till two of them showed error.

This job was resubmitted to the queue because it encountered a tool detected error condition on its compute resource.
TrimmomaticPE: Started with arguments: -threads 6 -phred33 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsang

what kind of error is this? and how can i fix it?

Thanks
Sihae

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Dear Sihae,
I am not sure based on the message. Check first your input files again. Are they in the right format?

You can either make an error report or share the history with me. Send me a message here in this forum and I give you my email address so you can share the history with me.

Cheers,
Florian

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This option designates that the reads are based on an earlier Illumina protocol version 1.3-1.7 (Phred+33 quality score scaling). The datatype for reads in that format is fastqillumina or fastqillumina.gz in Galaxy.

Your inputs are labeled as fastqsanger.gz. Both fastqsanger and the compressed version fastqsanger.gz have quality scores from Sanger/Illumina protocols 1.8 or higher (Sanger Phred+64 quality score scaling).

Try running FastQC on your reads. The report will note which quality score scaling was detected. The assigned datatype should match the content, or all sorts of odd issues/failures can result.

From a quick look, maybe the option “Perform initial ILLUMINACLIP step?” was set as “Yes” and the adaptor chosen is not an actual match for the protocol that created the reads, or the assigned datatype attribute metadata?

The first few FAQs here describe these different fastq formats in more detail. Most data is in fastqsanger/fastqsanger.gz now, and it is the fastq read datatype nearly all tools downstream from QA expect as an input, but you can confirm that with your own data, and make processing adjustments as needed. Galaxy Support

Plus I added a few tags to your topic that link to prior Q&A that explains these concepts with more even detail, tutorial links, etc that may be able to help.

@Flow will also be able to help with this and other potential issues by reviewing your history, but I wanted to give some help for what popped out for me as a potential data attribute vs content vs parameter problem that could lead to an error.

Update: There is another problem that you should address with priority first. There is a quota of one account per person at each distinct public Galaxy server. One account at each or all is fine, but not more than one at any. You currently have three older accounts and one new account at UseGalaxy.org. You must consolidate your data into one account, and download anything that doesn’t fit into one account that is still important to you. Which account you choose to use ongoing is your choice. Delete the others under User > Preferences immediately or all will be suspended by administrative processes. This can result in data loss, so please fix the problem yourself before that happens. How-to is explained here: Registering Accounts and here Account quotas. Write in to the mailing list in the FAQ should you need help with this.

Dear Florian

Thanks for the reply.

The data im trying to work with is already published. I think that might be easier for me to explain my problems.
I used PRJNA591665 study seq data.
Among them, SRR10538402 and SRR10538403 had problems with Trimmomatic. “perform initial ILLUMINACLIP step?” was set as “No”

This might be a very beginner’s question, How can I know the datatype?
I downloaded from ENA fastq.gz files and I didn’t know that it was fastqsanger.gz

In addition, like @jennaj recommended, i did run FastQC.
One of each data failed FastQC. Is this related to the datatype?

Thanks again for your attention.
Sihae

Dear Sihae,
Sorry for the late reply but I applied Trimmomatic and FastQC to the SRR10538402 data, which took quite some time to finish, and it worked for me. Can you please check that you have selected the newest version of the tools?

You actually know the sequence device and version from FastQC (first table, Sanger / Illumina 1.9 encoding) and it is also written that they have used the HiSeq X Ten device. So should be a newer Illumina version.

Cheers,
Florian

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Dear Florian
Thank you for your reply.
It worked for you? Im stumpt.
I used the latest Trimmomatic version which is 0.38.1
In case I tried different version(0.36.5) also but nothing works on those both data.
Could you recommend any other strategy i can try?

Thank
Sihae

Dear Sihae,
Instead of Trimmomatic you could use Cutadapt and TrimGalore. Maybe these tools work better for you. Else I can also offer to look at your history, but you would need to share it with me. If so send write me a message and I send you my email address.

Cheers,
Florian

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