Velocyto quits without error

[weishwu]

I tried to run velocyto run10x to generate loom from the outputs of a cellranger run. It successfully generated the cellsorted bam, but it quit during counting. I tried it twice but it failed again. The difference is that at the first time it failed at 80 million reads, and at 110 millions at the second time (the second run used the sorted bam from the first run so the sorting step was skipped).

My command line is:

velocyto run10x Sample_13-AB-2/ ./reference/refdata-cellranger-GRCh38-3.0.0/genes/genes.gtf 2>&1|tee > velocyto_sample_2.log &

The end of the log is:

2020-11-25 13:56:07,972 - DEBUG - Read first 110 million reads
2020-11-25 13:56:31,682 - DEBUG - Counting for batch 39, containing 100 cells and 1941663 reads
2020-11-25 13:58:19,543 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
2020-11-25 13:59:04,904 - DEBUG - Counting for batch 40, containing 100 cells and 1671230 reads
2020-11-25 14:00:38,156 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
2020-11-25 14:01:20,927 - DEBUG - Counting for batch 41, containing 100 cells and 1795289 reads
2020-11-25 14:02:54,326 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions

[xiejinghe]

Hi!

Have you had any luck solving this?

[Portulaca666]

Hi!

Have you had any luck solving this?

[xiejinghe]

Hi,

yes, already sloved.

However, I can not log in website right now because of network limitation. Could you please send me the question firstly? Maybe I can provide some clue for you.

Jinghe

发件人: wuzhigui 发送时间: 2022年1月11日 14:42 收件人: velocyto-team/velocyto.R 抄送: xiejinghe; Comment 主题: Re: [velocyto-team/velocyto.R] Velocyto quits without error (#159)

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