ENSEMBL annotations not populating correctly

[carnold-sjsu]

Hi, I'm running this pipeline from the SJSU HPC and I'm having an issue where ~8.5k out of my 29k rows of data are populating with both the symbol and genename as "NA". In a given NA row, there is a valid ENSEMBL ID that, if I look it up on ENSEMBL, leads to a valid gene product with an annotation that looks as though it is just not being populated correctly. I am running OSD-511 using the following script (using the cached files established on the spartan01 HPC by Jonathan Oribello):

NXF_SINGULARITY_CACHEDIR=/home/joribello/test_install/singularity nextflow run NF_RCP-F_1.0.3/main.nf -profile singularity,slurm -resume --gldsAccession GLDS-511 -c /home/joribello/test_install/cos_hpc_nextflow.config -c give_ALIGN_STAR_more_memory.config --runsheetPath /home/carnold/GLDS-511/Metadata/GLDS-511_bulkRNASeq_v1_runsheet.csv

The original runsheet was edited to correct the switched R1 and R2 files for one of the samples (they were entered incorrectly in the downloaded version from GL).
ALIGN_STAR_more_memory.config goes as follows:
process {
withName:'ALIGN_STAR' {
memory='45GB'
}
withName:'SORT_INDEX_BAM' {
memory='45GB'
}
withName: "COUNT_ALIGNED" {
maxRetries = 3
errorStrategy = 'retry'
memory = { 8.GB + 4.GB * task.attempt }
}
}

[asaravia-butler]

Hi @carnold-sjsu, will you please attach the following files:
/home/joribello/test_install/cos_hpc_nextflow.config
/home/carnold/GLDS-511/Metadata/GLDS-511_bulkRNASeq_v1_runsheet.csv

[carnold-sjsu]

Sure thing, here are those files. Thanks for getting back to me!
note: I changed the filetype of the .config file to .txt, since github doesn't support upload of .config files.
cos_hpc_nextflow.config.txt
GLDS-511_bulkRNASeq_v1_runsheet.csv

A quick note that I may lose access to the SJSU HPC and files from this run, as I believe they kick graduates out at some point!

[asaravia-butler]

Thanks, @carnold-sjsu. I don't see an issue with either of those files. I'd like to check a few more. Will you please send these two files to me?
NF_RCP-F_1.0.3/config/default.config
NF_RCP-F_1.0.3/config/software/by_docker_image.config

[carnold-sjsu]

Here you go.
default.config.txt
by_docker_image.config.txt