Error during spacemake run with the E13 mouse head dataset

[gianmore]

Hi,
I'm following your tutorial with the E13 mouse head dataset. During spacemake run the process failed several time even with the --.keep-going option. Looking at dge folder I can see that I have the different format of files for 9 out of the 12 tiles that you provided. In particular are missing data for 2517, 2617, 2618. Have you had this problem before? I have done the installation and different steps according to your protocol without problems. The only variation I have introduced is that in the spacemake environment I have installed also bcl2fastq from your bih-cubi channel. Can this create a conflict?

Error in group job b5aeb682-0225-4a2f-932d-420c4d5283da:
    [Mon Sep 16 12:36:54 2024]
    Error in rule create_dge:
        jobid: 85
        output: projects/openst_demo/processed_data/openst_demo_e13_mouse_head/illumina/complete_data/dge/dge.all.polyA_adapter_trimmed.mm_included.spatial_beads_fc_1_L3_tile_2618.txt.gz, projects/openst_demo/processed_data/openst_demo_e13_mouse_head/illumina/complete_data/dge/dge.all.polyA_adapter_trimmed.mm_included.spatial_beads_fc_1_L3_tile_2618.summary.txt
        shell:
        
        mkdir -p projects/openst_demo/processed_data/openst_demo_e13_mouse_head/illumina/complete_data/dge

        /igatech/rd/dev/Drop-seq_tools-2.5.1/DigitalExpression         -m 16g         I= projects/openst_demo/processed_data/openst_demo_e13_mouse_head/illumina/complete_data/final.all.polyA_adapter_trimmed.mm_included_fc_1_L3_tile_2618.bam        O= projects/openst_demo/processed_data/openst_demo_e13_mouse_head/illumina/complete_data/dge/dge.all.polyA_adapter_trimmed.mm_included.spatial_beads_fc_1_L3_tile_2618.txt.gz         SUMMARY= projects/openst_demo/processed_data/openst_demo_e13_mouse_head/illumina/complete_data/dge/dge.all.polyA_adapter_trimmed.mm_included.spatial_beads_fc_1_L3_tile_2618.summary.txt         CELL_BC_FILE=projects/openst_demo/processed_data/openst_demo_e13_mouse_head/illumina/complete_data/puck_barcode_files/spatialBarcodes_fc_1_L3_tile_2618.txt         CELL_BARCODE_TAG=CB         MOLECULAR_BARCODE_TAG=MI         TMP_DIR=/tmp         LOCUS_FUNCTION_LIST=INTRONIC READ_MQ=0
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

    [Mon Sep 16 12:36:54 2024]
    Error in rule filter_mm_reads:
        jobid: 87
        output: projects/openst_demo/processed_data/openst_demo_e13_mouse_head/illumina/complete_data/final.all.polyA_adapter_trimmed.mm_included_fc_1_L3_tile_2618.bam (pipe)
        shell:
        
        python /igatech/rd/dev/mambaforge/envs/spacemake/lib/python3.10/site-packages/spacemake/snakemake/scripts/filter_mm_reads.py             --in-bam projects/openst_demo/processed_data/openst_demo_e13_mouse_head/illumina/complete_data/final.polyA_adapter_trimmed.bam             --out-bam projects/openst_demo/processed_data/openst_demo_e13_mouse_head/illumina/complete_data/final.all.polyA_adapter_trimmed.mm_included_fc_1_L3_tile_2618.bam
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[danilexn]

Hi @gianmore

Sorry for the delayed response.

Can you please provide a trace of the error? We have not seen these issues with filter_mm_reads before, definitely not on that sample from the manuscript.

Let me know if there's anything else I can help with!

[gianmore]

I have fixed this, thanks.