Fatal error: Cannot open the file: reads.fa

[shimingt]

Hello there,

I have an error when I tried to run nonpareil:

tanshiming@S620100019205:~/Documents/nonpareil-trial$ nonpareil -s reads.fa -b output Nonpareil v3 [ 0.0] Counting sequences Fatal error: Cannot open the file: reads.fa [ 0.0] Fatal error: Cannot open the file: reads.fa

I have tried doing this on fasta and fastq files; the files are an illumina-trimmed dataset. Can someone please advice?

Thanks!

[gisleDK]

It sounds like the file, reads.fa, is not found. Try specifying exact path of reads.fa

[gunturus]

how did install nonpareil. Did you use the release or did you clone

[shimingt]

Hello @gunturus , I git cloned nonpareil. I did exactly everything that was mentioned on Nonpareil webpage, but I still got the error message.

[lmrodriguezr]

Is the file reads.fa present in ~/Documents/nonpareil-trial? Please do ls ~/Documents/nonpareil-trial and post the output.

[shimingt]

Hello Guys,

Sorry for the late reply. Here is the output:

tanshiming@S620100019205:~/Documents/nonpareil-trial$ ls ~/Documents/nonpareil-trial reads.fasta UPWRP0508161KA_TCCGGAGA-ATAGAGGC_L1L2_R1_001.fastq

My reads.fasta file is definitely in the same folder.

Any suggestions?

[gisleDK]

reads.fa ≠ reads.fasta