Closed hyunhwan-jeong closed 4 years ago
With the following script, I was able to run TraceQC v.0.1.0.
library(TraceQC)
library(fastqcr)
inp_file <- "~/TraceQC_test/inst/fastq/SRR4842510.fastq"
ref_file <- system.file("extdata", "test_data", "ref",
"ref.txt", package="TraceQC")
qc_dir <- "~/TraceQC_test/inst/fastqc"
fastqc("~/TraceQC_test/inst/fastq/",
qc.dir=qc_dir)
input_qc_path <- get_qcpath(inp_file, qc_dir)
obj <- TraceQC(input_file = inp_file,
ref_file = ref_file,
fastqc_file = input_qc_path,
ncores = 8)
generate_qc_report(
input_file = normalizePath(inp_file),
ref_file = normalizePath(ref_file),
fastqc_dir = normalizePath(qc_dir),
output_path = normalizePath("~/TraceQC_test/inst/output/SRR4842510.html"),
ncores = 8,
title = "TraceQC report abot SRR4842510",
preview = FALSE
)
I encountered errors for relative paths, so I used normalizePath
for the test run. It was okay, and I have revised the code to avoid the problem. I also got two warnings during the run.
Warning messages:
1: In normalizePath("~/TraceQC_test/inst/output/SRR4842510.html") :
path[1]="/mnt/data/hwan/TraceQC_test/inst/output/SRR4842510.html": No such file or directory
2: Removed 455 row(s) containing missing values (geom_path).
I will figure out how to resolve the normalizePath
issue.
The pass problem has been resolved with a new function(committed at c0178fb23d6658e7b90ad5a13efb72758a893959).
https://github.com/LiuzLab/TraceQC/blob/fc0bc86afcb9e4d2b879834c6ade2075f467c96b/R/util.R#L19-L24
After adding the parallelization code, it is now a way faster than before.
A single file processing took 10mins with 16 cores while the previous version took about two hours.
Originally posted by @hyunhwaj in https://github.com/LiuzLab/TraceQC/issues/5#issuecomment-636400960
I am going to test TraceQC with the files.