Is step1 complete? got message: "reading *_unaligned_R2.fastq not such file or directory"

[bmunozsa]

Hello, I've run vSNP step 1, and the program stopped after outputting this message "reading *_unaligned_R2.fastq not such file or directory". Why does this happens? Has the step1 finished correctly anyway?

Thanks in advance,

[stuber]

It may not be finding the input file. Is this at input? If possible send a screen shot showing working directory contents and command being used.

May try step 1 from a working directory containing just one sample (a single set of paired files)
vSNP_step1.py -r1 *_R1*.fastq.gz -r2 *_R2*.fastq.gz

[bmunozsa]

Thanks for finding the time to help me. Of course, this a screen shot from the folder before execution of the following line

vSNP_step1.py -r1 LOBO1_S6_L001_R1_001.fastq.gz -r2 LOBO1_S6_L001_R2_001.fastq.gz -r AY651334.fasta

and this is the message when the program stops

while this is the state of that same folder by that moment

[bmunozsa]

It may not be finding the input file. Is this at input? If possible send a screen shot showing working directory contents and command being used.

May try step 1 from a working directory containing just one sample (a single set of paired files) vSNP_step1.py -r1 *_R1*.fastq.gz -r2 *_R2*.fastq.gz

Do you think it would be useful to also share the actual files with you?

[stuber]

Yes, feel free to send me a link to the files at tod.p.stuber@usda.gov.