I am trying to taxonomic classify some RAW data of viruses using CLARK. For this, I have tried to install CLARK from CLARK's website following their README.

1. First I checked the quality of the virus paired-end reads by fasqc, then trimming, then using megahit assembler to assembly and generate final contigs. Store contigs in megahit_result folder.

(Example id: SRR10971381,SRR11903415)

2.

2i. #Download the zipped package of the latest CLARK release (i.e., v1.2.6.1), available from the CLARK webpage ("Download tab"). Or, you can do it by: $ wget http://clark.cs.ucr.edu/Download/CLARKV1.2.6.1.tar.gz

2ii. #Uncompress the package: $ tar -xzvf CLARKV1.2.6.1.tar.gz

2iii. #Install CLARK: $./CLARKSCV1.2.6.1/install.sh

2iv. To classify against viruses

$ ./CLARKSCV1.2.6.1/set_targets.sh clarkdb viruses --species

(Here, clarkdb becomes about 75GB and contain Custom, taxonomy, viruses_0, Viruses folders, and target.txt file.

2 v. To run CLARk on my assembly contigs data, I have used

$CLARK -k 31 -T ./clarkdb/targets.txt -D clarkdb -O samples.txt -R Clark_results -m 1 -n 32

samples.txt file contain my assemble data's path

(Here, k: k-mer length; T: filename of the targets definition; D: O: filename of objects; R: filename to store results; m: mode of execution(default:1); n: threads)

But i have faced problem to run CLARK, Here Error Message:

CLARK version 1.2.6.1 (UCR CS&E. Copyright 2013-2019 Rachid Ounit, rouni001@cs.ucr.edu) Loading database [clarkdb/db_central_k31_t10726_s1610612741_m0.tsk.*] ... Loading done (database size: 3086 MB read, with sampling factor 2) Mode: Default, Processing file: samples.txt, using 1 CPU. Failed to recognize the format of the file.

3

Or Analysis on raw data (not assembled data by assembler )

3i Paired end reads file name and data name

file name: samples.R.txt SRR10971381_1.fastq.gz SRR11903415._1fastq.gz

3ii

file name: samples.R.txt SRR10971381_1.fastq.gz SRR11903415._1fastq.gz

3iii Run CLARK on these datasets of paired-end reads (with option "-P"):

$ ./classify_metagenome.sh -P samples.R.txt samples.L.txt -R results.txt

Error message:

Would anyone please help me to run CLARK or to find out the problem and how I will solve the error?

Have any problems with CLARK database that I have downloaded or With the command that I have used?

Thank You