Help with error velocyto
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4 months ago
Chris ▴ 260

Hi Biostars,

I try to get the loom file and after trying I still don't know how to fix this error:

velocyto run -b MT/outs/filtered_feature_bc_matrix/barcodes.tsv -o output_dir -m Hg38_rmsk.gtf MT/outs/possorted_genome_bam.bam /cellranger/reference/refdata-cellranger-GRCh38
-3.0.0/genes/genes.gtf --samtools-memory 8000 --samtools-threads 8

MemoryError: bam file #0 could not be sorted by cells. This is probably related to an old version of samtools, please install samtools >= 1.6. In alternative this could be a memory error, try to set the --samtools_memory option to a value compatible with your system.
Otherwise sort manually by 
samtools sort -l [compression] -m [mb_to_use]M -t [tagname] -O BAM -@ [threads_to_use] -o cellsorted_[bamfile] [bamfile]

I have samtools 1.18 and sort bam file but still get the error:

samtools sort possorted_genome_bam.bam -o sorted.bam
samtools sort -t CB -O BAM -o cellsorted_possorted_genome_bam.bam possorted_genome_bam.bam

raise IOError("The bam file does not contain cell and umi barcodes appropriatelly formatted. If you are runnin UMI-less data you should use the -U flag.")
OSError: The bam file does not contain cell and umi barcodes appropriatelly formatted. If you are runnin UMI-less data you should use the -U flag.

I also tried some suggestion here:
https://github.com/velocyto-team/velocyto.py/issues/320.
Need help with Velocyto Analysis. Errors: MemoryError: bam file #0 could not be sorted by cells..

Thank you so much!

velocyto • 406 views
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Please edit your post and format it better. Code formatting should apply to all lines that were run on a terminal as well as terminal err/out. The rest of the lines should not be code formatted.

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