I got next error after run denoise command in my paired-end sequences
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
I have read and it is mentioned that this issue is when paired-ends are not well joined.
I have uploaded my demux.qzv file.
I used different parameters, soft and strong and I cannot understand why it is still happening.
You can add it anywhere after the qiime dada2 denoise-paired. The error you shared here indicates that you didn’t format the command correctly (don’t forget to include \ at the end of the line if you are splitting the commands across multiple lines, as you showed above).
Hi @amaria.gallego - --verbose won’t “fix” the command for you, it will return a lot of detailed “verbose” logging output - I need this output in order to help you (so that I can see what is going wrong). It looks like you copied some of that here, but please rerun and copy everything. You can use the command block I shared in my post above.
Actually, no need to rerun, even though you didn’t send everything, I think the key piece of information is right here:
Apparently one of you samples has one fewer reads in the forward direction than in the reverse. How were these sequences pre-processed, prior to DADA2?
Hi @amaria.gallego - --verbose won’t “fix” the command for you, it will return a lot of detailed “verbose” logging output - I need this output in order to help you (so that I can see what is going wrong). It looks like you copied some of that here, but please rerun and copy everything . You can use the command block I shared in my post above.
I know verbose wont fix the command, in fact I ran the command you provided before and I paste the ALL output above.
In the other hand respect to the pre-processed prior to DADA, I got an issue with one of my fastq files where you gave me an answer in other post. The issue was that I got an empty read thus I modified the fastq file removing this empty read. After that, the import in QIIME worked perfectly, so now the problem with DADA is because of that.
At this moment I am not sure how proceed
Great! I just wanted to make sure, since your comment above (“Still I am having the error”) sounded like you expected it to work after including --verbose - I realized I didn’t clarify what the --verbose flag was for, and wanted to make sure you knew - no offense was intended!
Strange - there should be a lot more to that error message - in the future I recommend that you carefully review all of the output before copying and pasting - and in general its usually better to send us too much information, rather than too little!
Ah yes, are you referring to this?
I’m not sure how you edited your file in order to fix it, but I suspect that it just postponed the actual issue. Have you specifically contacted the sequencing center and asked about that empty read? Your best bet is to solve the problem at the source - the raw sequencing data.