dtrudg
commented
1 year ago Hello, this doesn't look like a bug with Singularity, rather a usage question for a particular piece of software.
I would suggest asking for help on the Slack channels, or in the google group, links for which can be found at:
https://sylabs.io/singularity/
From the error messages, it's most likely you need to --bind mount a directory into the container, so that demuxify can write to a specific location. Singularity containers are read-only by default. However, I'm afraid that the developers here are not familiar with that software, and we don't have the resources to offer in-depth workflow specific troubleshooting.
There may be someone in the Slack channel or Google group who is already familiar with demuxify, and able to offer more assistance.
Hey I am trying to use Demuxify to run my single cell data with : singularity version 3.8.7-1.el7. I have de outputs in /CTL_scRNAseq/ :
-rw-rw-r-- 1 elenasl elenasl 710815 Nov 12 13:17 output_CTL_2.clust1.samples.gz -rw-rw-r-- 1 elenasl elenasl 58647272 Nov 12 13:17 output_CTL_2.clust1.vcf.gz -rw-rw-r-- 1 elenasl elenasl 1084565 Nov 12 12:49 output_CTL_2.lmix -rw-rw-r-- 1 elenasl elenasl 311049 Nov 11 13:41 pileup_CTL_2.cel.gz -rw-rw-r-- 1 elenasl elenasl 169391056 Nov 11 14:01 pileup_CTL_2.plp.gz -rw-rw-r-- 1 elenasl elenasl 2103906973 Nov 11 13:59 pileup_CTL_2.umi.gz -rw-rw-r-- 1 elenasl elenasl 67295060 Nov 11 14:01 pileup_CTL_2.var.gz
when I run:
[elenasl@cicngs RNAseq_TLR4_TLR3]$ singularity exec Demuxafy.sif Combine_Results.R -o /CTL_scRNAseq/combined_results.tsv -f /CTL_scRNAseq/ -u /CTL_scRNAseq/SOUPORCELL_OUTDIR --solo /CTL_scRNAseq/SOLO_OUTDIR --scds /data/elenasl/scRNAseq/CTL_scRNAseq/SCDS_OUTDIR
System has not been booted with systemd as init system (PID 1). Can't operate.
Failed to connect to bus: Host is down
Creating directory as it doesn't exist. Complete path: /CTL_scRNAseq/
Warning message:
In dir.create(gsub(basename(args$out), "", args$out), recursive = TRUE) : cannot create dir '/CTL_scRNAseq', reason 'Read-only file system' Reading in freemuxlet results.
Can't read in the freemuxlet report either from the file you provided or to find the '*.samples.gz' file in the directory you provided. Please double check your path and provide the full path to the freemuxlet file. Exiting.
What OS/distro are you running NAME="CentOS Linux" VERSION="7 (Core)" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="7" PRETTY_NAME="CentOS Linux 7 (Core)" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:7" HOME_URL="https://www.centos.org/" BUG_REPORT_URL="https://bugs.centos.org/"
CENTOS_MANTISBT_PROJECT="CentOS-7" CENTOS_MANTISBT_PROJECT_VERSION="7" REDHAT_SUPPORT_PRODUCT="centos" REDHAT_SUPPORT_PRODUCT_VERSION="7"
How did you install Singularity from the source.