Another permissions question about galig HOT 6 CLOSED

Dear Rachel,
can you share with us the log files, the input files you have used, and the complete command line that you have used?
We would also want to know the operating system you used and the docker version.
May you also check that you have enough free disk space?

from galig.

Hi,

Sure, I used this command, and definitely have enough free disk space:

docker run -v "$PWD"/asgalgw_data:/data algolab/asgal:v1.1.3

Logs:

salmon_index.log
salmon_quant.log

Operating system seems to be:

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"

FASTQ files are somewhat large, but I'm using the following reference inputs:

http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz
http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/GRCh37.p13.genome.fa.gz
http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.pc_transcripts.fa.gz

Thanks for the help,

Rachel

from galig.

Hi Rachel,
from what I can see (also from samtools sort doc), I would say that it's a problem of space. samtools sort stores a lot of temporary files in the current directory (it kinda splits the bam into multiple files before merging them into the final sorted bam). To avoid this, it's necessary to define the tmp directory to use (using -T).

The fastest and easiest solution is to cd to a directory where you know you have space (like the parent folder of the output folder you are using for running asgal) and then run asgal from there.

The other solution would be to update asgal code to allow user to define a temporary directory (but this'll take more time).

Let us know if this solves your issue.

Best.
Luca

from galig.

Rachel,
can you please run the following command and report if it works?

docker run -v "$PWD"/asgalgw_data:/data algolab/asgal:v1.1.6

from galig.

Hi, yes, this seems to be working!

It's still running, but generating samtools.71.8476.tmp.0000.bam etc, in the asgalgw_data/ directory.

Thanks!

Rachel

from galig.

Yes, that was the intended effect.
Previously the location of the temporary files depended on the docker installation.

I am closing this bug, feel free to open another issue if any problem arises.

from galig.