#Error# Pipeline exited with error code 1

[rafia...@gmail.com]

Hei

Thanks for making a very useful tool. I recently installed Metatrans and ran the test data with out any problem (with -nde option). I am using Ubuntu 16.04

However when I use the -nde -tax option, I get the following error. I do have usearch installed and link created at /usr/local/bin to the installation folder

#Running sample 'C1JB3ACXX_1_5':
/home/rafi/Downloads/metatrans/test/0-Software/scripts/getMeta.py:184: VisibleDeprecationWarning: Reading unicode strings without specifying the encoding argument is deprecated. Set the encoding, use None for the system default.
  mydata = np.genfromtxt(filename,names=True,dtype=None,delimiter='\t')   #Get table-data. Note: "#SampleName" is taken as "SampleName" without "#".
/home/rafi/Downloads/metatrans/test/0-Software/scripts/getMeta.py:184: VisibleDeprecationWarning: Reading unicode strings without specifying the encoding argument is deprecated. Set the encoding, use None for the system default.
  mydata = np.genfromtxt(filename,names=True,dtype=None,delimiter='\t')   #Get table-data. Note: "#SampleName" is taken as "SampleName" without "#".
/home/rafi/Downloads/metatrans/test/0-Software/scripts/getMeta.py:184: VisibleDeprecationWarning: Reading unicode strings without specifying the encoding argument is deprecated. Set the encoding, use None for the system default.
  mydata = np.genfromtxt(filename,names=True,dtype=None,delimiter='\t')   #Get table-data. Note: "#SampleName" is taken as "SampleName" without "#".
    #Running Module3 >>Mapping16S (taxonomical analysis)<< ... (Date: '23-01-19' Time: '16h:18m:07s CET')

 #Error# Pipeline exited with error code 1.

I looked further and in the log file under usearch directory under the processed sample I get the following error

"Invalid command line

Unknown option cluster"

Could you help me figure this out. 

which usearch
/usr/local/bin/usearch

Thanks in advance.

Regards

Rafi

[metatr...@gmail.com]

Hi Rafi,

According to the output you show, it seems like "usearch" is accessible, it is only complaining regarding the option "cluster".

Probably you have a newer version of "usearch" which doesn't account for this option in favor of another option configuration.

The "cluster" option was used for usearch v5.X. If you use, for instance, usearch v.8, you should check the calls to "usearch"

within "run_mapX.sh" files and change them for something like:

...  usearch  \
    -cluster_fast $fin \
    -uc $fout1 \
    -id 0.97 \
    -threads $THREADS \
    -centroids $fout2 \
    -consout $fout3 \
    -sort length

...

Regarding the other warnings we are almost sure that are caused because you are using a newer version of Python and their libs, and

some methods/functions might be deprecated.

We are sorry but we cannot provide much more help right now. Anyway we hope these comments help you go further.

Greeetings

[metatr...@gmail.com]

Hello,

If you are able to call "usearch" using " -cluster_fast" from the command line alone, it seems like

you might have a syntax typo in the call to usearch within "run_map_16s.sh". Check backslashes

used to break the command are properly set. After the command break character "\" make sure no other blank char or any

other hidden char is typed after it.

Greetings

On 29 de gen. 2019 13:53 AM UTC+1, rafia...@gmail.com wrote:

Thank you for your reply. I have been busy with a grant application, so could try your suggestion today.

In the run_map.sh file I could not find the call to usearch. However, there was usearch call in run_map_16s.sh file and changed it to what you have suggested. Now is get the error

../run_map_16s.sh: -cluster_fast: not found

#Error# Pipeline exited with error code 127.

IBased on usearch documentation I think the -cluster_fast option is correct. Do you think I need to add a usearch call in the run_map.sh file and if so where.

Thanks

Rafi