search

CPTR-ReSeqTB / UVP

Mycobacterium tuberculosis next generation sequence analysis
MIT License
21 stars 12 forks source link

rm: cannot remove ‘Results/test/kraken/kraken.txt’: No such file or directory #4

Closed matnguyen closed 5 years ago

matnguyen commented 5 years ago

It seems that UVP is trying to remove a file that has already been moved. This is what I see in the log file:

---[ mv ]---
Command: 
mv Results/test QC

---[ rm ]---
Command: 
rm Results/test/kraken/kraken.txt

Standard Error: 
rm: cannot remove ‘Results/test/kraken/kraken.txt’: No such file or directory

I am running UVP with the --keepfiles flag

mezewudo commented 5 years ago

Seems the Kraken tool in your installation did not run as expected. Make sure you install Krkaken correctly, following their user manual and check to see it outputs the required results.

matnguyen commented 5 years ago

Kraken runs properly and the outputs are present. It is just that the files that are in Results/test (which include the kraken.txt) are moved to the QC directory. UVP then tries to remove Results/test/kraken/kraken.txt which has already been moved to QC. The kraken.txt is actually in QC/kraken/kraken.txt