SNP pipeline error

[SingleronHH]

HI:
I am trying the celescope_test_script on celescope_test_data using SNP pipeline. I had this error in the middle of the run:

bcftools: symbol lookup error: /opt/conda/envs/saturn/envs/celescope/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv

I installed Celescope from github follow the instructions from here: https://github.com/singleron-RD/CeleScope/blob/master/docs/installation.md.

$ git clone https://github.com/singleron-RD/CeleScope.git
$ cd CeleScope
$ conda install mamba
$ mamba create -n celescope -y --file conda_pkgs.txt
$ conda activate /opt/conda/envs/saturn/envs/celescope
$ pip install celescope

then install reference db

celescope rna mkref
--thread 32
--genome_name Homo_sapiens_ensembl_99
--fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa
--gtf Homo_sapiens.GRCh38.99.gtf

then install SNP db
celescope snp mkref
--thread 32
--genome_name Homo_sapiens_ensembl_99
--fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa

then run the run_shell.sh under the celescope_test_script/snp/
a folder named "shell" was generated and a sh script was in it.

then I run the sh script under the "shell" dir from the celescope_test_script/snp/ dir.

everything was fine and the GATK was finished successfully.

the error came out when the pipeline tried to use bcftools to call the variants.

2022-09-20 03:35:07,085 - celescope.tools.step.debug_subprocess_call - INFO - bcftools mpileup -f /home/jovyan/git/CeleScope/hs_ensembl_99/Homo_sapiens.GRCh38.dna.primary_assembly.fa --threads 4 --annotate DP,AD -d 100000000 -o .//test1/07.variant_calling/test1_raw.bcf .//test1/07.variant_calling/test1_splitN.bam --regions-file /opt/conda/envs/saturn/envs/celescope/lib/python3.9/site-packages/celescope/data/snp/panel/lung_1.bed
bcftools: symbol lookup error: /opt/conda/envs/saturn/envs/celescope/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv

please advise how to solve this issue.

Thanks you very much for your help!

[SingleronHH]

BTW: when I tried to run the bcftools, the error show up. It seems that the error is due to bcftools

bcftools
bcftools: symbol lookup error: /opt/conda/envs/saturn/envs/celescope/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv

[SingleronHH]

BTW:
do you have docs for maple?
as I found in the celescope_test_script, the test1.mapfile contains
snp ../../celescope_test_data/snp/fastqs test1 ../../celescope_test_data/snp/snp_match_dir

I can understand snp part, but what is the rest "test1 ../../celescope_test_data/snp/snp_match_dir"?

thank you very much for your help!

[zhouyiqi91]

Similar issue here: bcbio/bcbio-nextgen#3632

BTW: when I tried to run the bcftools, the error show up. It seems that the error is due to bcftools

bcftools
bcftools: symbol lookup error: /opt/conda/envs/saturn/envs/celescope/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv

[zhouyiqi91]

BTW: do you have docs for maple? as I found in the celescope_test_script, the test1.mapfile contains snp ../../celescope_test_data/snp/fastqs test1 ../../celescope_test_data/snp/snp_match_dir

I can understand snp part, but what is the rest "test1 ../../celescope_test_data/snp/snp_match_dir"?

thank you very much for your help!

https://github.com/singleron-RD/CeleScope/blob/master/docs/snp/multi_snp.md#arguments
4th column: The 4th column has different meaning for each assay. The single cell rna directory after running CeleScope is called matched_dir