Data Import error message

[tiger815]

Bcbio nextgen ver 1.2.3. R 4.0.2

Hi~ I'm getting a lot of help from your awesome package.

I found one error in this package. When loading bcbio RNA-seq data after executing standard bulk RNAseq, an error seems to occur because the combined.counts file was missing. This file was placed in a folder called featureCounts, a subfolder of the final folder. I copied the combined.counts file from the featureCounts folder to the upper folder to solve the error. After that, I had no problem loading the data.

Bcbio nextgen ver 1.2.3. R 4.0.2

Thanks,

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GeneID, normalization : move annotated.count file up to directory..

object1 <- bcbioRNASeq( uploadDir = ("/data/home/tiger815/seq_raw_data/ipsc_CM_doxo/samples/final"), caller = "star", level = "genes", organism = "Homo sapiens", genomeBuild = "hg38" )

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── bcbioRNASeq ─────────────────────────────────────────────────────────────────────────────── Importing bcbio-nextgen RNA-seq run

── Run info ──

uploadDir: /data/home/tiger815/seq_raw_data/ipsc_CM_doxo/samples/final projectDir: 2020-09-15_samples

→ Sanitizing sample names: DOXO-1nM_rep1, DOXO-1nM_rep2, DOXO-1nM_rep3, DOXO-5nM1, DOXO-5nM2, DOXO-5nM3, DOXO-cont1, DOXO-c..... 9 samples detected: ● DOXO_1nM_rep1 ● DOXO_1nM_rep2 ● DOXO_1nM_rep3 ● DOXO_5nM1 ● DOXO_5nM2 ● DOXO_5nM3 ● DOXO_cont1 ● DOXO_cont2 ● DOXO_cont3

→ Importing project-summary.yaml at /data/home/tiger815/seq_raw_data/ipsc_CM_doxo/samples/final/2020-09-15_samples using yaml::yaml.load_file(). → Importing data_versions.csv at /data/home/tiger815/seq_raw_data/ipsc_CM_doxo/samples/final/2020-09-15_samples using vroom::vroom(). → Importing programs.txt at /data/home/tiger815/seq_raw_data/ipsc_CM_doxo/samples/final/2020-09-15_samples using vroom::vroom(). → Importing bcbio-nextgen.log at /data/home/tiger815/seq_raw_data/ipsc_CM_doxo/samples/final/2020-09-15_samples using readr::read_lines(). → Importing bcbio-nextgen-commands.log at /data/home/tiger815/seq_raw_data/ipsc_CM_doxo/samples/final/2020-09-15_samples using readr::read_lines().

── Sample metadata ──

→ Getting sample metadata from YAML. → Getting sample quality control metrics from YAML.

── Counts ──

── featureCounts → Slotting aligned counts into primary counts() assay. → Importing aligned counts from featureCounts. Error in import(file = file.path(projectDir, "combined.counts")) : Assert failure. [1] isAFile(file) || isAURL(file) is not TRUE.

[mjsteinbaugh]

Ah thanks, the directory structure has been reorganized a bit with the bcbio-nextgen v1.2.3 release. I'll fix this in bcbioRNASeq to reflect the featureCounts directory change.

[mjsteinbaugh]

@tiger815 Can you paste the directory structure of the bcbio output using tree? I'm setting up a new test run to check the changes in bcbio v1.2.3.

The featureCounts matrix has been moved from bcbio/YYYY-MM-DD_bcbio/combined.counts to bcbio/YYYY-MM-DD_bcbio/featureCounts/combined.counts, and we need to reflect this change in the R code.

[tiger815]

Hi @mjsteinbaugh, Sure.

This is the result of 'tree' executed in 'final' directory of Bcbio bulk RNAseq output directory. I hope it helps to fix the bug.

. ├── 2020-09-15_samples │?? ├── counts │?? ├── featureCounts │?? ├── multiqc │?? │?? ├── multiqc_data │?? │?? └── report │?? │?? └── metrics │?? ├── tpm │?? └── transcriptome ├── DOXO-1nM_rep1 │?? ├── qc │?? │?? ├── fastqc │?? │?? ├── qualimap_rnaseq │?? │?? │?? └── DOXO-1nM_rep1 │?? │?? │?? └── css │?? │?? ├── salmon │?? │?? ├── samtools │?? │?? └── star │?? ├── salmon │?? │?? ├── aux_info │?? │?? │?? └── bootstrap │?? │?? ├── libParams │?? │?? └── logs │?? └── STAR ├── DOXO-1nM_rep2 │?? ├── qc │?? │?? ├── fastqc │?? │?? ├── qualimap_rnaseq │?? │?? │?? └── DOXO-1nM_rep2 │?? │?? │?? └── css │?? │?? ├── salmon │?? │?? ├── samtools │?? │?? └── star │?? ├── salmon │?? │?? ├── aux_info │?? │?? │?? └── bootstrap │?? │?? ├── libParams │?? │?? └── logs │?? └── STAR ├── DOXO-1nM_rep3 │?? ├── qc │?? │?? ├── fastqc │?? │?? ├── qualimap_rnaseq │?? │?? │?? └── DOXO-1nM_rep3 │?? │?? │?? └── css │?? │?? ├── salmon │?? │?? ├── samtools │?? │?? └── star │?? ├── salmon │?? │?? ├── aux_info │?? │?? │?? └── bootstrap │?? │?? ├── libParams │?? │?? └── logs │?? └── STAR ├── DOXO-5nM1 │?? ├── qc │?? │?? ├── fastqc │?? │?? ├── qualimap_rnaseq │?? │?? │?? └── DOXO-5nM1 │?? │?? │?? └── css │?? │?? ├── salmon │?? │?? ├── samtools │?? │?? └── star │?? ├── salmon │?? │?? ├── aux_info │?? │?? │?? └── bootstrap │?? │?? ├── libParams │?? │?? └── logs │?? └── STAR ├── DOXO-5nM2 │?? ├── qc │?? │?? ├── fastqc │?? │?? ├── qualimap_rnaseq │?? │?? │?? └── DOXO-5nM2 │?? │?? │?? └── css │?? │?? ├── salmon │?? │?? ├── samtools │?? │?? └── star │?? ├── salmon │?? │?? ├── aux_info │?? │?? │?? └── bootstrap │?? │?? ├── libParams │?? │?? └── logs │?? └── STAR ├── DOXO-5nM3 │?? ├── qc │?? │?? ├── fastqc │?? │?? ├── qualimap_rnaseq │?? │?? │?? └── DOXO-5nM3 │?? │?? │?? └── css │?? │?? ├── salmon │?? │?? ├── samtools │?? │?? └── star │?? ├── salmon │?? │?? ├── aux_info │?? │?? │?? └── bootstrap │?? │?? ├── libParams │?? │?? └── logs │?? └── STAR ├── DOXO-cont1 │?? ├── qc │?? │?? ├── fastqc │?? │?? ├── qualimap_rnaseq │?? │?? │?? └── DOXO-cont1 │?? │?? │?? └── css │?? │?? ├── salmon │?? │?? ├── samtools │?? │?? └── star │?? ├── salmon │?? │?? ├── aux_info │?? │?? │?? └── bootstrap │?? │?? ├── libParams │?? │?? └── logs │?? └── STAR ├── DOXO-cont2 │?? ├── qc │?? │?? ├── fastqc │?? │?? ├── qualimap_rnaseq │?? │?? │?? └── DOXO-cont2 │?? │?? │?? └── css │?? │?? ├── salmon │?? │?? ├── samtools │?? │?? └── star │?? ├── salmon │?? │?? ├── aux_info │?? │?? │?? └── bootstrap │?? │?? ├── libParams │?? │?? └── logs │?? └── STAR └── DOXO-cont3 ├── qc │?? ├── fastqc │?? ├── qualimap_rnaseq │?? │?? └── DOXO-cont3 │?? │?? └── css │?? ├── salmon │?? ├── samtools │?? └── star ├── salmon │?? ├── aux_info │?? │?? └── bootstrap │?? ├── libParams │?? └── logs └── STAR

[mjsteinbaugh]

This should be fixed in bcbioRNASeq v0.3.39! Apologies for the delay in pushing the bug fix.

See related pull request https://github.com/hbc/bcbioRNASeq/pull/164