Kristoffer

Ok, thanks! Attached is the full 500 simulated dataset. I'll try on a larger simulation and let you know. [TSPY_simulated_500.txt](https://github.com/TulsaBioinformaticsToolsmith/MeShClust/files/1843419/TSPY_simulated_500.txt)

I get the same error message for datasets with the same simulation parameters but with 2500 and 12500 sequences as well. When I try with the parameter `--align` I get...

Great that works, thanks!

Ok, great. It should work with multiple cores using the `run_isoncorrect --t 20` command. Let me know how it goes.

If you have a few very large clusters, you can(/should) use `--split_wrt_batches`. According to the documentation, this option ``` --split_wrt_batches Process reads per batch (of max_seqs sequences) instead of per...

If the file `/tmp/tmpl_shyp5i/split_in_batches/100000_0.fastq` is still there, could you try running: ``` /usr/bin/time /home/eniac/miniconda3/envs/isoncorrect/bin/isONcorrect --fastq \ /tmp/tmpl_shyp5i/split_in_batches/100000_0.fastq --outfolder 03-correction/100000_0 \ --exact_instance_limit 50 --max_seqs 2000 --k 9 --w 20 --xmin 18...

Perhaps `isONcorrect` also logs the error for this in a file `.stderr` somewhere in the output older in `03-correction/100000_0`. I forgot if i Implemented that. In that case you could...

The error you reported is just because the file is not there anymore (these files get flushed from the tmp folder regularly by the system). It is not the actual...

Not sure why you have a symbolic link to the file? You need to copy it completely `cp /tmp/tmpzgp8a2tb/split_in_batches/100000_0.fastq THE_FAILING_TMP_FILE.fastq`. At the moment you only seem to have a symbolic...

Okay, how about this. On line 218 in `run_isoncorrect` [here](https://github.com/ksahlin/isONcorrect/blob/master/run_isoncorrect#L218), please change this line to `tmp_work_dir = "XX-correction/"` (or whatever path you want on your system). This way all the...