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csoneson / alevinQC

Create QC and summary reports for Alevin output
https://csoneson.github.io/alevinQC/
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Input directory not compatible with Salmon v0.14 or newer (without external whitelist), the following required file(s) are missing or malformed: #17

Closed PavanKhosla closed 4 years ago

PavanKhosla commented 4 years ago

Hi @csoneson,

Would you happen to know why I am receiving the following error message?

Thank you!

Best, Pavan

Versions:

R - 4.0 alevinQC - 1.4.0 salmon - 1.3.0

R code:

library(alevinQC)

setwd("C:/Users/pavan/Alevin/08_04/alevin_1k/")

alevinQCReport(baseDir = system.file("/alevin_output/alevin/", package = "alevinQC"), sampleId = "alevin_test_full", outputFile = "alevinReport.html", outputFormat = "html_document", outputDir = "../", forceOverwrite = TRUE)

Error Message:

Error in checkAlevinInputFiles(baseDir) : Input directory not compatible with Salmon v0.14 or newer (without external whitelist), the following required file(s) are missing or malformed: C:\Users\pavan\Documents\R\win-library\4.0\alevinQC/alevin/raw_cb_frequency.txt C:\Users\pavan\Documents\R\win-library\4.0\alevinQC/alevin/featureDump.txt C:\Users\pavan\Documents\R\win-library\4.0\alevinQC/aux_info/meta_info.json C:\Users\pavan\Documents\R\win-library\4.0\alevinQC/aux_info/alevin_meta_info.json C:\Users\pavan\Documents\R\win-library\4.0\alevinQC/cmd_info.json C:\Users\pavan\Documents\R\win-library\4.0\alevinQC/alevin/whitelist.txt

Input directory not compatible with Salmon v0.14 or newer (with external whitelist), the following required file(s) are missing or malformed: C:\Users\pavan\Documents\R\win-library\4.0\alevinQC/alevin/raw_cb_frequency.txt C:\Users\pavan\Documents\R\win-library\4.0\alevinQC/alevin/featureDump.txt C:\Users\pavan\Documents\R\win-library\4.0\alevinQC/aux_info/meta_info.json C:\Users\pavan\Doc

Alevin Code:

~/github.com/COMBINE-lab/salmon/releases/download/v1.3.0/salmon-latest_linux_x86_64/bin/salmon alevin -lISR -1 pbmc_1k_v2_fastqs/pbmc_1k_v2_S1_L001_R1_001.fastq.gz pbmc_1k_v2_fastqs/pbmc_1k_v2_S1_L002_R1_001.fastq.gz -2 pbmc_1k_v2_fastqs/pbmc_1k_v2_S1_L001_R2_001.fastq.gz pbmc_1k_v2_fastqs/pbmc_1k_v2_S1_L002_R2_001.fastq.gz --chromium -i index -p 32 -o alevin_output --tgMap txp2gene.tsv --dumpFeatures

Data:

https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_1k_v2

csoneson commented 4 years ago

It looks like a problem in the specification of the baseDir in the alevinQC call. Using system.file as you do above essentially tells R to look for the data inside the alevinQC package. Instead, just do baseDir = "alevin_output" to point alevinQC to the output directory.

PavanKhosla commented 4 years ago

Thank you so much!!!