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velocyto-team / velocyto.R

RNA velocity estimation in R
http://velocyto.org
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No loom file generated, no error output #125

Open yanwengong opened 4 years ago

yanwengong commented 4 years ago

I have used RNA velocity before without any problem. However, when I tried to analyze a new set of data with the same code, I cannot get the loom file generated. There is no informative information in the output file or error file. I tried both "velocyto run" and "velocyto run10x". It would generate several cellsorted_bam.bam.tmp.bam but seems to have issue merging them and didn't output any error. I am going to sort with samtosls first and tried again, but want to post the issue here to see whether anyone knows the reason. Please see the code and the last part of output file below.

code: velocyto run -b /pub/yanweng/opportunity_award/data/stem_ctrl/outs/filtered_gene_bc_matrices/MMulatta/barcodes.tsv -o /pub/yanweng/opportunity_award/data/stem_ctrl/velocyto -m /pub/yanweng/common_data/macaca_mulatta/rheMac8_rmsk.gtf /pub/yanweng/opportunity_award/data/stem_ctrl/outs/possorted_genome_bam.bam /pub/yanweng/common_data/macaca_mulatta/Macaca_mulatta.Mmul_8.0.1.97.gtf

tail of output log file: 2020-02-22 11:46:17,519 - INFO - Load the repeat masking annotation from /dfs3/pub/yanweng/common_data/macaca_mulatta/rheMac8_rmsk.gtf 2020-02-22 11:46:17,519 - DEBUG - Reading /dfs3/pub/yanweng/common_data/macaca_mulatta/rheMac8_rmsk.gtf, the file will be sorted in memory 2020-02-22 11:48:21,012 - DEBUG - Processed masked annotation .gtf and generated 4416468 intervals to mask! 2020-02-22 11:48:21,407 - INFO - Scan /dfs3/pub/yanweng/opportunity_award/data/stem_ctrl/outs/possorted_genome_bam.bam to validate intron intervals 2020-02-22 11:48:24,935 - DEBUG - Reading /dfs3/pub/yanweng/opportunity_award/data/stem_ctrl/outs/possorted_genome_bam.bam 2020-02-22 11:48:25,105 - DEBUG - Read first 0 million reads 2020-02-22 11:48:25,105 - DEBUG - Marking up chromosome 1 2020-02-22 11:53:55,080 - DEBUG - Read first 10 million reads 2020-02-22 11:59:40,231 - DEBUG - Read first 20 million reads 2020-02-22 12:01:58,118 - DEBUG - Marking up chromosome 2

SiyiWanggou commented 4 years ago

@yanwengong Are you using the data from 10X Chromium samples? The filtered_gene_bc_matrices folder seems to be the results of cellranger. If so, you should follow the instruction for 10X.