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MaestSi / MetONTIIME

A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework
GNU General Public License v3.0
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folder 4e does not exist #66

Closed joyleng closed 1 year ago

joyleng commented 1 year ago

Hi

Sorry me again. I manage to run MetONTIIME but was getting an error that I see a couple of people have had before. When it got to trying to calculate diversity measures it would error saying that table-collapsed-absfreq-level6.qza does not exist. So I re-downloaded MetONTIIME as suggested on other discussions as my initial download was probably about a month ago. However I am now getting a different error nearly straight away:

ERROR ~ Error executing process > 'importDb (1)'

Caused by: java.io.IOException: Cannot run program "qsub" (in directory "/pub63/joyl/MetONTIIME/work/4e/885217e0535be2262e3291d3c8a2c1"): error=2, No such file or directory

I have checked and the folder 4e does not exist within the work folder. I don't know if this is linked with specifying the singularity.cacheDir on line 72 of the .conf file? I had a search and I couldn't find anyone else who has had this error. I have attached the nextflow log file which states the error in full. .nextflow.log

Many thanks Joy

MaestSi commented 1 year ago

Hi, based on this discussion we had before, it seems you didn't have pbspro job scheduler, and you should change executor = pbspro to executor = local in metontiime2.conf file. Best, SM

joyleng commented 1 year ago

Ah yes that's working now. I think I had made that change to the .conf during out previous discussion but as I downloaded everything again I had missed changing it on the new one.

Thanks again Joy

MaestSi commented 1 year ago

Ok! Ciao, SM