ERROR when running dnbc4tools rna
Closed this issue · 13 comments
Hi there,
I am trying to run the v3.0 demo data online https://db.cngb.org/search/sample/CNS1063416/. Errors showed up when running the dnbc4tools rna run using singularity during the count process. The error message is as follows.
2024-05-08 02:33:38,378 - INFO - Merge beads within the same droplet based on correlation values.
2024-05-08 02:33:38,378 - INFO -
2024-05-08 02:33:45,405 - INFO - Generate beads and merge corresponding cell id files /data1/mgi_10x_scrna_comparison/mgi/mouse_brain_1/02.count/barcodeTranslate.txt.
2024-05-08 02:33:45,405 - INFO -
2024-05-08 02:34:06,890 - count - INFO - Executing command: /opt/conda/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/software/tagAdd -n 32 -bam /data1/mgi_10x_scrna_comparison/mgi/mouse_brain_1/01.data/final_sorted.bam -file /data1/mgi_10x_scrna_comparison/mgi/mouse_brain_1/02.count/ba
rcodeTranslate.hex.txt -out /data1/mgi_10x_scrna_comparison/mgi/mouse_brain_1/02.count/anno_decon_sorted.bam -tag_check CB:Z: -tag_add DB:Z:
2024-05-08 02:44:28,883 - count - INFO - Program costs: 622s
input bam: /data1/mgi_10x_scrna_comparison/mgi/mouse_brain_1/01.data/final_sorted.bam
file: /data1/mgi_10x_scrna_comparison/mgi/mouse_brain_1/02.count/barcodeTranslate.hex.txt
output bam: /data1/mgi_10x_scrna_comparison/mgi/mouse_brain_1/02.count/anno_decon_sorted.bam
tag check: CB:Z:
tag add: DB:Z:
nthreds: 32
2024-05-08 02:44:28,884 - count - INFO - Executing command: /opt/conda/envs/dnbc4tools/bin/samtools index -@ 32 /data1/mgi_10x_scrna_comparison/mgi/mouse_brain_1/02.count/anno_decon_sorted.bam
2024-05-08 02:45:08,781 - count - INFO -
2024-05-08 02:45:08,782 - count - INFO - Executing command: /opt/conda/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/software/PISA count -one-hit -@ 32 -cb DB -anno-tag GN -umi UB -list /data1/mgi_10x_scrna_comparison/mgi/mouse_brain_1/02.count/cell.id -outdir /data1/mgi_10x_scrna_comp
arison/mgi/mouse_brain_1/02.count/raw_matrix /data1/mgi_10x_scrna_comparison/mgi/mouse_brain_1/02.count/anno_decon_sorted.bam
2024-05-08 02:45:08,798 - count - ERROR - Command failed with exit code 127
2024-05-08 02:45:08,798 - count - ERROR - /opt/conda/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/software/PISA: error while loading shared libraries: libcurl.so.4: cannot open shared object file: No such file or directory
What's the solution for this?
Best!
Gary
docker or singularity version？
singularity version 3.4.1-4.2.ohpc.1.3.9
try
singularity shell dnbc4tools.sif
/opt/conda/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/software/PISA count -h
Same error showed up
Singularity dnbc4tools.sif:~/tools> /opt/conda/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/software/PISA count -h
/opt/conda/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/software/PISA: error while loading shared libraries: libcurl.so.4: cannot open shared object file: No such file or directory
Can you see this libcurl.so.4 in the /opt/conda/envs/dnbc4tools/lib/
Singularity dnbc4tools.sif:/opt/conda/envs/dnbc4tools/lib> ls libcurl*
libcurl.so libcurl.so.4 libcurl.so.4.8.0
singularity exec dnbc4tools.sif dnbc4tools --version
2.1.2
your ~/.bashrc have export LD_LIBRARY_PATH ?
If there is, comment it out and then open a new window to run the singularity PISA count -h command.
No, there is not.
.bashrc
Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
Uncomment the following line if you don't like systemctl's auto-paging feature:
export SYSTEMD_PAGER=
User specific aliases and functions
export PATH=$HOME/cellranger-7.2.0:$PATH
export PATH=$HOME/cellranger-dna-1.1.0:$PATH
>>> conda initialize >>>
!! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/data1/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/data1/miniconda3/etc/profile.d/conda.sh" ]; then
. "/data1/miniconda3/etc/profile.d/conda.sh"
else
export PATH="/data1/miniconda3/bin:$PATH"
fi
fi
unset __conda_setup
<<< conda initialize <<<
And I run singularity using slurm, would that be an issue? But the same error showed up in singularity shell.
I think it's not related. I need time to test it.
Or you can use the conda version first. I haven't found this problem with my singularity, so it may take more time to find the problem.
the conda version works without error