makeSummary.sh not recognizing estimate_abundance.sh output

[marisol ortiz]

Hello there, 

I am trying to use the makeSummaryTable script to create tables for several of my samples. I have several .csv files from runs of estimate_abundance that I have visualized in KronaTools, but I wanted to use the makeSummary Table for more information. Here is the script I passed and the output it gave me.

Input: 

$ makeSummaryTables.sh 10 5 /projectnb/cnidaria/mdot/Analysis_Tools/CLARKSCV1.2.6.1/48_Mangrove/48MResults.csv /projectnb/cnidaria/mdot/Analysis_Tools/CLARKSCV1.2.6.1/93_Mangrove/93MResults.csv /projectnb/cnidaria/mdot/Analysis_Tools/CLARKSCV1.2.6.1/95_Mangrove/95MResults.csv

Output:

$Failed to read /projectnb/cnidaria/mdot/Analysis_Tools/CLARKSCV1.2.6.1/48_Mangrove/48MResults.csv. Please check the pathname and that it is a correct CLARK report file.

Failed to read /projectnb/cnidaria/mdot/Analysis_Tools/CLARKSCV1.2.6.1/93_Mangrove/93MResults.csv. Please check the pathname and that it is a correct CLARK report file.

Failed to read /projectnb/cnidaria/mdot/Analysis_Tools/CLARKSCV1.2.6.1/95_Mangrove/95MResults.csv. Please check the pathname and that it is a correct CLARK report file.

Files: TableSummary_per_Report.csv and TableSummary_HitCount.csv were generated.

So I went to the .csv files that produced perfectly good results.krn files and it had Object_ID, Length, Assignment. Not really sure what to do.

Would love some help, 

Marisol 

[Rachid]

Hi Marisol!

Thank you for posting!

In order to run the script "makeSummaryTable" you need to pass the files generated by "estimate_abundance".

Could you please run it again for those files instead and let us know ?

Thank you,

Best,

Rachid

[marisol ortiz]

Hi Rachid, 

I realized the problem was that the estimate_abundance.sh script does not produce a .csv file like the website says it does. There is no option for an output, so the abundace estimations just print to the screen and are not saved. I tried to just copy the read out into a .csv file but then I got a segmentation error. Perhaps I just downloaded something wrong?

Let me know and thanks so much for getting back to me!

Marisol

[Rachid]

Marisol,

The results produced by "estimate_abundance.sh" are in the CSV format and generated in the standard output, so you can just redirect that into a file of your choosing (i.e., "> filename.csv").

I hope this helps. Let me know if you have more questions?

Best,

Rachid

[marisol ortiz]

Hi Rachid, 

so I would run for example 
$estimate_abundance.sh -D DIR_DB/ -F /projectnb/cnidaria/mdot/Analysis_Tools/CLARKSCV1.2.6.1/TestResults.csv >TestResults_Estimate_Abundace.csv 

?

Thanks again for the help

Marisol

[Rachid]

Yes.

Anytime!