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rajewsky-lab / openst

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab
https://rajewsky-lab.github.io/openst/
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e13 Preprocessing transcriptomic library encounter pipefail #68

Open guijie2015 opened 3 days ago

guijie2015 commented 3 days ago

Hi,when I`m running example data on the Preprocessing transcriptomic library step, I encounter the problem.

98adec7c81a075a584e7f534f283f83

Here is the log file. log.log

I understand you're busy, but if you have some time, I would really appreciate your help with this issue.

Steps to reproduce the bug

# Sample code to reproduce the bug
ref_path=/home/data/hejunjie/16.openST_20241014/ref
spacemake init --dropseq_tools /home/data/hejunjie/16.openST_20241014/1.e13_mouse_head_test_20241014/1.spacemake/openst_e13_mouse_head_demo/bins/Drop-seq_tools-2.5.4

spacemake config add_species \
   --name mouse \
   --reference genome \
   --sequence ${ref_path}/GRCm39vM30.genome.fa \
   --annotation ${ref_path}/gencodevM30.annotation.gtf

spacemake config add_species \
   --name mouse \
   --reference rRNA \
   --sequence ${ref_path}/mouse.rRNA.fa

spacemake config add_species \
   --name mouse \
   --reference phiX \
   --sequence ${ref_path}/phiX.fa

spacemake projects add_sample --project_id openst_demo \
    --sample_id openst_demo_e13_mouse_head \
    --R1 e13_mouse_head_R1_001.fastq.gz e13_mouse_head_reseq_R1_001.fastq.gz \
    --R2 e13_mouse_head_R2_001.fastq.gz e13_mouse_head_reseq_R2_001.fastq.gz \
    --species mouse \
    --puck openst \
    --run_mode openst \
    --barcode_flavor openst \
    --puck_barcode_file e13_mouse_head_tiles/*.txt.gz \
    --map_strategy "bowtie2:phiX->bowtie2:rRNA->STAR:genome:final"

spacemake run --cores 32 --keep-going

Environment info

danilexn commented 3 days ago

Hi, and thanks for the very detailed report.

We have noticed this issue in the spacemake automated_analysis, and a bugfix is in progress.

For the rest of the Open-ST workflow, these reports are not really necessary. You can make sure the rest of the pipeline runs by using --keep_going flag in spacemake.

I hope this helps, and sorry for the inconvenience!

Dani

guijie2015 commented 3 days ago

Hi, and thanks for the very detailed report.

We have noticed this issue in the spacemake automated_analysis, and a bugfix is in progress.

For the rest of the Open-ST workflow, these reports are not really necessary. You can make sure the rest of the pipeline runs by using --keep_going flag in spacemake.

I hope this helps, and sorry for the inconvenience!

Dani

Very thanksful for your reply. But I am very sorry fot that when I am trying using '--keep_going' and then running the next step Pairwise alignment. It told me I miss the dge.all.polyA_adapter_trimmed.mm_included.spatial_beads_puck_collection.h5ad file. 图片

How can I create this dge.all.polyA_adapter_trimmed.mm_included.spatial_beads_puck_collection.h5ad.

Here is my Pairwise alignment code. openst from_spacemake --project-id openst_demo --sample-id openst_demo_e13_mouse_head merge_modalities

danilexn commented 3 days ago

That probably means you used the default spacemake mode that runs meshing before stitching the puck_collection, therefore that file will not be available. You have to generate it using openst from_spacemake ... spatial_stitch, take a look here:

https://rajewsky-lab.github.io/openst/latest/computational/pairwise_alignment/#tissue-transcriptome

Under "My run_mode and/or puck do not look like that"

guijie2015 commented 2 days ago

spatial_stitch

Very thanksful for your reply. I try running these code openst from_spacemake --project-id openst_demo\ --sample-id openst_demo_e13_mouse_head\ spatial_stitch\ --tile-coordinates fc_1_coordinate_system.csv then get this error. 图片

under my dge directory，I have these files. I can`t find "fc_1_tile_2267.h5ad dge.fc_1_tile_2268.h5ad", which is running spatial_stitch in manual on the example 图片 图片