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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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KeyError: 'MB1' ' returned non-zero exit status 1. when running scRNA-seq analysis for indropv3 #3740

Open juychen opened 9 months ago

juychen commented 9 months ago

Version info

To Reproduce Exact bcbio command you have used:

bcbio_nextgen.py /usersdata/junyichen/data/risi_0201/risi_0201/endo_rishi.yaml -n 20

Your yaml configuration file:

details:
- algorithm:
    cellular_barcode_correction: 1
    minimum_barcode_depth: 1000
    sample_barcodes: /usersdata/junyichen/data/risi_0201/risi_0201/barcodes_given.txt
    # transcriptome_fasta: /home/jholab/genomes/Hsapiens/hg38/rnaseq/ref-transcripts.fa
    # transcriptome_gtf: /home/jholab/genomes/Hsapiens/hg38/rnaseq/ref-transcripts.gtf
    umi_type: harvard-indrop-v3
  analysis: scRNA-seq
  description: Endometrioma_rishi_0201
  files:
  - /usersdata/junyichen/data/risi_0201/risi_0201/SUB15154_R1.fastq.gz
  - /usersdata/junyichen/data/risi_0201/risi_0201/SUB15154_R2.fastq.gz
  - /usersdata/junyichen/data/risi_0201/risi_0201/SUB15154_R3.fastq.gz
  - /usersdata/junyichen/data/risi_0201/risi_0201/SUB15154_R4.fastq.gz
  genome_build: hg38
  metadata: {}
fc_name: endometrioma_rishi_0201
upload:
  dir: /usersdata/junyichen/output/risi_0201/final

Log files (could be found in work/log) Please attach (10MB max): bcbio-nextgen-commands.log, and bcbio-nextgen-debug.log.

bcbio-nextgen-commands.log

bcbio-nextgen-debug.log

juychen commented 9 months ago

I suspect that it is the problem caused by the umis package. https://github.com/vals/umis I have tried to downgrade the umis 1.0.8 to 1.0.7 in the anaconda environment of bcbio and then the error did not occur.