When I try to run the Rsubread commands subjunc or align in Studio, I get the error "Input files have different amount of reads.
subjunc (index="~/Documents/HarvardLincs/myindedx", readfile1="~/Documents/HarvardLincs/SRR120607501.fastq.gz", readfile2="~/Documents/HarvardLincs/SRR120607502.fastq.gz", outputfile="BT549.bam",nthreads = 8)
ERROR: two input files have different amounts of reads! The program has to terminate and no alignment results were generated!
Error in .load.delete.summary(output_file[i]) : Summary file BT549.bam.summary was not generated! The program terminated wrongly!
sessionInfo() R version 4.0.1 (2020-06-06) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.5
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:  en_US.UTF-8
attached base packages:  stats graphics grDevices utils datasets methods base
other attached packages:  Rsubread_2.2.2
loaded via a namespace (and not attached):
 compiler4.0.1 Matrix1.2-18 tools4.0.1 tinytex0.24 grid4.0.1
 xfun0.15 lattice_0.20-41
I get the same error message for several fastq files that I downloaded from GEO. Is it true that all these files have a data problem, or is this some other issue?