Problem with DRAGEN RNAseq hashtable directory

Question

[yussab]

Dear all,

Recently I wrote a code to work with DRAGEN and RNAseq pipeline. I use this command:

/opt/edico/bin/dragen -f -l \
         -r refdir \
         -1 ${forward} \
         -2 ${reverse} \
         -a ${gtf} \
         --output-dir output/${sample} \
         --output-file-prefix ${sample} \
         --RGID ${sample}_group_id \
         --RGSM ${sample} \
         --enable-rna true \
         --enable-rna-gene-fusion true

I get back a this error:

  ERROR: The specified hashtable directory cannot be used to run RNA: refdir    Regenerate the hashtable with "--build-hash-table true" and "--ht-build-rna-hashtable true"

The problem is that my refdir was generated with this flags, I've tried a lot of different workaround but the result doesn't change.

This is the command that I've used to build the has table:

 Automatically generated by dragen version 01.003.044.4.0.3. Command line: /opt/edico/bin/dragen --ht-reference refdir/ref_genome.fa --output-directory output/ref --build-hash-table true --ht-build-rna-hashtable true --ht-mask-bed  /opt/edico/fasta_mask/hg38_alt_mask.bed Hash table version 8

I really have no clue about what could it be the error, I hope to find someone that has my same issue.

Thanks in advance!

Best regards,
Youssef

[GenoMax]

Since this is such a specific thing (and not many are going to have access to this hardware) your best bet is to email Illumina tech support.

Answer 1

[DBScan]

Can't you just download the reference genome from here? DRAGEN Reference

I've never had the need to generate my own hashtable.

[yussab]

Thank you DBScan, this seen to be a good option.

But I still have one problem , I have downloaded the last version, but it gives me this error:

ERROR: Hash table refdir is version 9 - version 8 is required

The problem here is that when I try to download the version 8, it downloads a file named

hg38+alt_masked+cnv+graph+hla+rna-8-r2.0-1.run

I can't find a tar.gz from their webpage, I found another page but they have the same links (https://emea.support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform/product_files.html) , furthermore I have no clue about this file.run and can find any information online.

Thank you in advance for your help!

[yussab]

I found it was a script, I hate this absence of documentation

[GenoMax]

ERROR: Hash table refdir is version 9 - version 8 is required

Looks like you may not be running the latest version of DRAGEN?

[yussab]

Dear DBScan ,

I have downloaded the reference directory from the website, extract it and give it as input refdir.

ls dragen_hg38_v8_graph

total 8.0G

anchored_hla hash_table.cfg hash_table.cmp info.json mask.bed ref_index.bin reference.bin str_table.bin anchored_rna hash_table.cfg.bin hash_table_stats.txt kmer_cnv.bin md5sum ref_pop_snps.bin repeat_mask.bin

Unfortunately it continues to give me the same error as before:

Regenerate the hashtable with "--build-hash-table true" and "--ht-build-rna-hashtable true"

I run the command :

 /opt/edico/bin/dragen -f -l \
         -r dragen_hg38_v8_graph \
         -1 ${forward} \
         -2 ${reverse} \
         -a ${gtf} \
         --output-dir output/${sample} \
         --output-file-prefix ${sample} \
         --RGID ${sample}_group_id \
         --RGSM ${sample} \
         --enable-rna true \
         --enable-rna-gene-fusion true

[DBScan]

You should upgrade to DRAGEN 4.2 if you are able to.