LotuS2 Error: Missing LotuS_progout.log

[atfdh]

Hello, I was trying to run the below command for analyzing full-length ITS sequences: ./lotus2 -i /my/PacBioDir/ -s configs/sdm_PacBio_ITS.txt -m PacBioDir/my_PacBio.map -o /my/PacBio/LotuS2 -p PacBio -id 0.97 -CL cdhit -refDB UNITE -forwardPrimer XYZ -reversePrimer XYZ ... but encountered an error related to LotuS_progout.log, while in the LotuSLogS directory, there is only LotuS_cmds.log and LotuS_run.log. How can I figure it out?

Thanks for any help

[hildebra]

Hey, hmm this is a strange error, did you install lotus2 via conda or via git clone? in the latter case, please make sure you run ./autoInstall.pl does the example work? "./lotus2 -i Example/ -m Example/miSeqMap.sm.txt -o myTestRun"

[atfdh]

Hi, Initially, I attempted to install lotus2 via Conda. Although the installation process appeared to complete successfully and I activated the environment, I couldn't find the 'lotus2' directory or the 'sdm_src' subdirectory. That is why I installed it via git clone.

However, when I tried to run './autoInstall.pl', I encountered a permission denied error. I managed to execute the script using 'perl autoInstall.pl'. Additionally, when attempting to run the provided example, I received the following warning: 'WARNING: No forward PCR primer for amplicon found in mapping file (column header "ForwardPrimer"). This might invalidate chimera checks.'

[hildebra]

This sounds like a problem with the sysadmin (missing writing permission), might be good to check with your local sysadmin what is going on (although lotus2 was devised to work in non-admin mode). the warning is normal, as long as you get the output that should be fine (also see README for further examples, and how to avoid that warning). So once the example runs correctly and you get outputs, try lotus2 again. Can you try to execute lotus2 with your own from the lotus2 dir, this might solve some of the problems you described.