Paired-end reads classify_metagenome

[Guilherme Liberato da Silva]

Hi!

I'm trying to classify metagenome in CLARK but received a error message after finished, telling that "Error: Paired-ended reads must be in FASTQ files". However the command I am using is:

./classify_metagenome.sh -P /79070_TGACCA_S1_L003_TYR /sampleR1.txt /79070_TGACCA_S1_L003_TYR /samplesR2.txt -R resultsclarkTYR.txt

Where sampleR1.txt holds:
/79070_TGACCA_S1_L003_TYR /79070_cleanlines_R1_TYR.fastq
 

and sampleR2.txt holds:

/79070_TGACCA_S1_L003_TYR /79070_cleanlines_R2_TYR.fastq

Which can be the problem? What exactly we should put inside .txt file? 

Could I put instead of sampleR1.txt and samplesR2.txt put directly the Fastq files? And, the results must be in .txt file?

Please, could you help me? Thanks!

Cheers

[Rachid OUNIT]

Please check the content of your files "/79070_TGACCA_S1_L003_TYR /79070_cleanlines_R1_TYR.fastq" and "/79070_TGACCA_S1_L003_TYR /79070_cleanlines_R2_TYR.fastq". CLARK will use them if they have indeed the fastq format.

If they do and the issue is persistent then please feel free to share these files with us so we can reproduce the issue on our side.

Cheers,

Rachid

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