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error at assembly (flye step) #9
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Hi Paul, This is a Flye error that seems to be linked to a high read coverage (1017) which could confuse Flye, it is similar to this issue: Here are some suggestions from the author of Flye: Cam you try to rerun after modifying the nextflow.config file line 90 to reduce the coverage for initial disjointig assembly: Hope this helps. |
HI, I keep having a similar issue. |
@maddne No the assembly.fasta is an output file of the Flye step. Work dir: Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named Can you check the content of .command.sh and .command.run inside the work dir? |
@vmurigneu yes I can check the content them. They seem to appear hidden and I cannot upload them directly, so I copied the content into a txt file |
@maddne have you checked that you have permission to write in the output folder? Did the previous steps of the pipeline generated expected output (trimming, filtering)? Can you send the command line used and content of nextfow.config please |
I assumed that I had problems with permission however I changed the permission to the output folder to drwxrwxrwx, but this wasn't the case, because it was able to write files there. The previous steps Trimming and filtering worked like a charm and produced output and HTML report. Here are some reports: Here is my command nextflow main.nf --samplesheet /home/bio/micropipe/micropipe/samples5.csv --fastq /home/bio/micropipe/micropipe/bact5/ --outdir /home/bio/micropipe/micropipe/results123/ --datadir /home/bio/micropipe/micropipe/bact5/ nextflow.config file was downloaded as in your repo and I only changed the cache folder for singularity at line 3 |
@maddne would you please be able to post the .command.run inside the work dir |
I am working with a student who is having this issue with their execution of nextflow
Looking for some guidance on how to proceed.
Best,
Paul
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