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dragen's Issues

Not enough space left in /tmp during covid pipeline installation

Dear Dragen support,
I am trying to install Dragen covid pipeline as described in the guide.

Here is the code

download the installer

cd /staging
wget https://webdata.illumina.com/downloads/software/dragen/install_dragen-covid-pipeline-RUO-1.1.0.run
chmod +x /staging/install_dragen-covid-pipeline-RUO-v1.1.0.run

install docker Engine described in this link.

sudo yum install -y yum-utils
sudo yum-config-manager \
	--add-repo \
	https://download.docker.com/linux/centos/docker-ce.repo

sudo yum install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin

sudo systemctl start docker

install dragen_covid_pipeline

 ./install_dragen-covid-pipeline-RUO-1.1.0.run 

Verifying archive integrity...  100%    100%   All good.
Uncompressing dragen-covid-pipeline 1.1.0
Not enough space left in /tmp (6299332 KB) to decompress ./install_dragen-covid-pipeline-RUO-1.1.0.run (8561976 KB)
Use --nodiskspace option to skip this check and proceed anyway
Consider setting TMPDIR to a directory with more free space.

Partition Info

[root@localhost tmp]# df -h
Filesystem      Size  Used Avail Use% Mounted on
/dev/md126p7     15G  8.7G  6.1G  59% /
devtmpfs        126G     0  126G   0% /dev
tmpfs           126G  316K  126G   1% /dev/shm
tmpfs           126G   11M  126G   1% /run
tmpfs           126G     0  126G   0% /sys/fs/cgroup
/dev/nvme0n1p1  5.9T   75G  5.8T   2% /staging
/dev/md126p2     49G   33M   49G   1% /home
/dev/md126p6     30G  672M   29G   3% /var
/dev/md126p1    497M  139M  359M  28% /boot
/dev/md126p8    9.8G  148M  9.7G   2% /var/log
/dev/md126p10   4.9G   71M  4.9G   2% /var/log/audit
tmpfs            26G     0   26G   0% /run/user/0

demo test: single_fastq_in_bam_out.sh

if I open the script single_fastq_in_bam_out.sh I can read this

#!/bin/bash
/opt/edico/bin/dragen -f -r /staging/examples/reference/hg19/hg19.fa.k_21.f_16.m_149  -1 /staging/examples/reads/SRA056922_30x_rand1_100K.fastq --RGID DRAGEN_RGID --RGSM DRAGEN_RGSM --output-directory /staging/examples/ --output-file-prefix SRA056922_30x_rand1_100K

In actual version of dragen 07.021.645.4.0.3 The path of the references are in /staging/human and not /staging/examples

image

Bcl_in_fastq_out.sh

I tried to run demo script to generate fastQ file from BCL folder.
here is the status of the test:
image
Here is the content of bcl_in_fastq_out.sh script

#!/bin/bash
mkdir -p /staging/examples/fastq
cd /staging/examples/fastq
/opt/edico/bin/dragen --bcl-conversion-only=true --bcl-input-directory /mnt/san/131022_hsxten008_0123_FC543 --output-directory /staging/examples/fastq
~

Check the input folder in ls /mnt/ /mnt/san/ does not exist

find 131022_hsxten008_0123_FC543 folder in /opt, /staging and /mnt

find: ‘131022_hsxten008_0123_FC543’: No such file or directory

Enable MultiGenome Hash Table Builder

Dear Marwa,
to enable the custom Multigenome Hash Table Builder we need 4 files as specified in this command:

dragen --build-hash-table true \
       --ht-graph-vcf-list <path to a text file containing newline-separated phased VCF file names> \
       --ht-reference <reference.fasta> \
       --ht-graph-bed < graph.bed> \
       --ht-mask-bed <mask.bed> \
       --output-directory <DIR>

The Documentation of Inputs forwards us to download page.

  1. How to Set of population VCF?

  2. Reference Genome
    2.1. Which fasta reference we need to download if we work with hg38?

  1. Where are Graph bed file and Mask bed file ? are there in zipped folder of Illumina DRAGEN Graph Reference Genome hg38 (alt-masked_graph+cnv+hla+rna_v2) — For DRAGEN v4.0 ? indicated by masked_graph?

Thanks
Karim

Dragen server: deb versus rpm distribution

Dear Judy,
I run the docker image of OL8.ISO like described in README.

  • The last release seems to bea clone of Clonezilla which seems to be based on Debian distribution.
  • For example the Clonezilla Live 3.0.1 is the latest stable version of this Debian-based live system for disk imaging/cloning tasks based on the powerful Clonezilla software.
  • The default OL8 ISO indicated in these instructions seems to be using apt package manager and not rpm/dnf packages
  • python2 seems to be pre-installed

image

  • During installation, it said to me that the dragen is built for el8 and not RedHat el8.

image

Thanks

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