Souporcell determination of cell origin

[Gh-Genetics]

Dear Doctor， I used a VCF file that mixed 400 samples to distinguish the source of cells. The script ran without any issues, but did not produce a result file that could be judged. I would like to ask what is the reason for this.

Here is my script: singularity exec ./souporcell_latest.sif souporcell_pipeline.py \ -i ./possorted_genome_bam.bam \ -b ./filtered_feature_bc_matrix/barcodes.tsv.gz \ -f ./ensembl_cow_genome/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa \ -t 2\ -o ./cellranger_V6_matrix_bam \ -k 2 --common_variants ./genes_overlap.vcf

Screenshot of my VCF file section:

my VCF file: After I run the script:

[wheaton5]

It did not finish. I see intermediate files that would have been deleted if it finished. Look at the .err files for any error.

[Gh-Genetics]

It's over. There are no errors reported in the file. err. The final result is only the intermediate file

	谭光辉（GuangHui-Tan）

西北农林科技大学动物科技学院，Northwest A&F University 17585473094 | ---- Replied Message ---- | From | Haynes @.> | | Date | 7/25/2023 12:51 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [wheaton5/souporcell] Souporcell determination of cell origin (Issue #194) |

It did not finish. I see intermediate files that would have been deleted if it finished. Look at the .err files for any error.

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[wheaton5]

Well it still didnt finish. Did the top level process produce any errors? How did it finish? Did you pipe the stdout and stderr to a file or just printed to the console? Did you run this remotely? If so, without nohup it may have been killed when the connection was killed.

[Gh-Genetics]

when i use： demuxlet --sam /work/home/luo_funong/Tan_Guang-hui/single_cell_RNA/cow_developmental_stage/cellranger_V6_matrix_bam/C5_3_TP/possorted_genome_bam.bam \ --tag-group CB \ --tag-UMI UR \ --vcf /work/home/luo_funong/Tan_Guang-hui/single_cell_RNA/cow_developmental_stage/genes_overlap_with_header.vcf\ --field GT \ --out /work/home/luo_funong/Tan_Guang-hui/single_cell_RNA/cow_developmental_stage/publishCattle.leiqiongSNPs.recode.vcf

FATAL ERROR - [E:] Your VCF/BCF files and SAM/BAM/CRAM files does not have any matching chromosomes, or some chromosome names are duplicated

And I use： singularity exec /work/home/luo_funong/Tan_Guang-hui/mutai_qufen/Demuxafy.sif souporcell_pipeline.py \ -i /work/home/luo_funong/Tan_Guang-hui/single_cell_RNA/cow_developmental_stage/cellranger_V6_matrix_bam/C5_3_TP/possorted_genome_bam.bam \ -b /work/home/luo_funong/Tan_Guang-hui/single_cell_RNA/cow_developmental_stage/cellranger_V6_matrix_bam/C5_3_TP/raw_feature_bc_matrix/barcodes.tsv.gz \ -f /work/home/luo_funong/Tan_Guang-hui/placenta_RNA/ensembl_cow_genome/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa \ -t 2 \ -o /work/home/luo_funong/Tan_Guang-hui/single_cell_RNA/cow_developmental_stage/cellranger_V6_matrix_bam/C5_3_TP_soupcell_comon_snp \ -k 2 \ --common_variants /work/home/luo_funong/Tan_Guang-hui/single_cell_RNA/cow_developmental_stage/genes_overlap_with_header.vcf

There were no errors reported, and the task was not cancelled. After all runs were completed, there were only intermediate files. I got the same situation after rerunning it many times. I am submitting tasks from nodes

	谭光辉（GuangHui-Tan）

西北农林科技大学动物科技学院，Northwest A&F University 17585473094 | ---- Replied Message ---- | From | Haynes @.> | | Date | 7/25/2023 12:59 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [wheaton5/souporcell] Souporcell determination of cell origin (Issue #194) |

Well it still didnt finish. Did the top level process produce any errors? How did it finish? Did you pipe the stdout and stderr to a file or just printed to the console? Did you run this remotely? If so, without nohup it may have been killed when the connection was killed.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[wheaton5]

This is not a souporcell issue. This is likely an hpc cluster issue.

And as for the demuxlet error, you must be using a different version of the reference fasta as you have used for your common variants file.