Hello, I am setting up FVE to run for the first time. Thank you for creating this program, I am excited about its utility! On my first attempt to run the test data set, I got this error:
Finished parsing inputs.
Error: The sam file FastViromeExplorer-reads-mapped-sorted.sam is empty. Please check the kallisto and samtools version. Please use kallisto 0.43.1 and samtools 1.4 or later.
## I checked the versions of both, I'm wondering if the reason I'm getting this error is because I installed Kallisto and Samtools with miniconda? Thanks for your advice.
index Builds a kallisto index
quant Runs the quantification algorithm
bus Generate BUS files for single-cell data
pseudo Runs the pseudoalignment step
merge Merges several batch runs
h5dump Converts HDF5-formatted results to plaintext
inspect Inspects and gives information about an index
version Prints version information
cite Prints citation information
Running kallisto without arguments prints usage information for
(base) :~/FastViromeExplorer$ samtools -version
[main] unrecognized command '-version'
(base) :~/FastViromeExplorer$ samtools --version
samtools 1.7
Using htslib 1.7
Copyright (C) 2018 Genome Research Ltd.
(base) :~/FastViromeExplorer$ which samtools
/home/usr/miniconda3/bin/samtools
(base) :~/FastViromeExplorer$ which kallisto
/home/usr/miniconda3/bin/kallisto
(base) :~/FastViromeExplorer$
Hello, I am setting up FVE to run for the first time. Thank you for creating this program, I am excited about its utility! On my first attempt to run the test data set, I got this error:
(base) : $ java -cp bin FastViromeExplorer -1 ~/FastViromeExplorer/test/reads_1.fq -2 ~/FastViromeExplorer/test/reads_2.fq -i ~/FastViromeExplorer/test/GOV-viral-populations/GOV_viral_populations.idx -l ~/FastViromeExplorer/test/GOV-viral-populations/gov_viral_populations-length.txt -o test-output
Finished parsing inputs. Error: The sam file FastViromeExplorer-reads-mapped-sorted.sam is empty. Please check the kallisto and samtools version. Please use kallisto 0.43.1 and samtools 1.4 or later.
## I checked the versions of both, I'm wondering if the reason I'm getting this error is because I installed Kallisto and Samtools with miniconda? Thanks for your advice.
(base) :~/FastViromeExplorer$ kallisto -version Error: invalid command -version kallisto 0.46.2
Usage: kallisto [arguments] ..
Where can be one of:
Running kallisto without arguments prints usage information for
(base) :~/FastViromeExplorer$ samtools -version [main] unrecognized command '-version' (base) :~/FastViromeExplorer$ samtools --version samtools 1.7 Using htslib 1.7 Copyright (C) 2018 Genome Research Ltd. (base) :~/FastViromeExplorer$ which samtools /home/usr/miniconda3/bin/samtools (base) :~/FastViromeExplorer$ which kallisto /home/usr/miniconda3/bin/kallisto (base) :~/FastViromeExplorer$