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When I try to run the quantification code
#!/bin/bash
for fn in data/DRR0161{25..40};
do
samp=basename ${fn}
echo "Processing sample ${samp}"
salmon quant -i athal_index -l A
-1 ${fn}/${samp}_1.fastq.gz
-2 ${fn}/${samp}_2.fastq.gz
-p 8 --validateMappings -o quants/${samp}_quant
done
even though the files are there, in the data directory, the tool seems to not recognize the fastq files and pops the following error for every DRR0161xx_x.fastq.gz file:
ERROR: file [DRR016140_2.fastq.gz] does not appear to exist!
]
salmon quant was invoked improperly
Is this some common error or is it a new bug?
Thanks in advance for any response/suggestion on how to proceed here
The text was updated successfully, but these errors were encountered:
Hi,
I just installed salmon using conda. I tried to execute the sample test that comes on the main page: https://combine-lab.github.io/salmon/getting_started/
When I try to run the quantification code
#!/bin/bash
for fn in data/DRR0161{25..40};
do
samp=
basename ${fn}
echo "Processing sample ${samp}"
salmon quant -i athal_index -l A
-1 ${fn}/${samp}_1.fastq.gz
-2 ${fn}/${samp}_2.fastq.gz
-p 8 --validateMappings -o quants/${samp}_quant
done
even though the files are there, in the data directory, the tool seems to not recognize the fastq files and pops the following error for every DRR0161xx_x.fastq.gz file:
ERROR: file [DRR016140_2.fastq.gz] does not appear to exist!
]
salmon quant was invoked improperly
Is this some common error or is it a new bug?
Thanks in advance for any response/suggestion on how to proceed here
The text was updated successfully, but these errors were encountered: