cellranger count matrix

Question

[shamza]

Hello everyone,

I am trying to run the cell ranger count using the following command.

cellranger-7.1.0/cellranger count \
  --id project1 \
  --transcriptome refdata-gex-mm10-2020-A \
  --fastqs NK_dataset/ \
  --sample 1013MJ1,1013MJ2,1013Saline1,1013Saline2,106MJ1,106MJ2,106Saline1,106Saline2,113MJ-1,113MJ-2,113Saline1,113Saline2 \
  --expect-cells 85000 \
  --localcores 8 \
  --localmem 100

I am using doing this on the cluster and due to some reason my file did not go through. The pipestance would run and gives me output of the following files.

__1_project.mro

and a folder with the following files,

SC_RNA_COUNTER_CS  _invocation  _jobmode  _lock  _log  _mrosource  _tags  _timestamp  _uiport  _uuid  _versions  journal  tmp

I am not sure what I am doing wrong here, can someone help me figure this out?

Thank you!

[Ram]

Please follow up on your previous posts or they - including this one - will be removed.

• retaining only the clusters of interest
• velocyto.R installation

[Ram]

There has to be an error message being printed on the screen. What does it say?

[shamza]

My data was very big and it take a couple of hours to run 1 sample and I had many. So I left it running and checked it 10, 12, and 24 hours later it was working fine. but then there was a power outage for a couple of minutes I am not sure if that could be the reason, but I was using a cluster computer it should still have kept running.

[Ram]

but then there was a power outage for a couple of minutes I am not sure if that could be the reason, but I was using a cluster computer it should still have kept running.

Email your sysadmin and check if the outage affected the HPC

[shamza]

I contacted them and it turns out it was due the power outage.

[Pilon]

Hello, I am facing the same problem as you.. I have tried unplugging the computer and rebooting, but is still giving the same problem. How were you able to fix the problem?

[ATpoint]

OP problem was due to a local hardware that we cannot debug or help with. You need to add relevant information for help. "same" is a vague term.

[Pilon]

Below is the code I used to run cellranger count matrix.

run_id="01_163963-S4" 
fastq_path="/media/bequiet/Analysis/60-935425408/00_Rawdata" 
sample_id="163963-S4" ref_path="/media/bequiet/Analysis/refdata/refdata-gex-mm10-2020-A"

cellranger count --id=$run_id --fastqs=$fastq_path --sample=$sample_id --transcriptome=$ref_path

Using the same code, I was able to get output of:

01_163963-S2.mri.tgz  _invocation  outs               _sitecheck  _vdrkill
_cmdline              _jobmode     _perf              _tags       _versions
_filelist             _log         _perf._truncated_  _timestamp
_finalstate           _mrosource   SC_RNA_COUNTER_CS  _uuid 60-847914058_SEQ_REPORT.pdf   60-847914058.md5

However, after the electricity outage (or there could be other possible reasons),

 01_163963-S4.mri.tgz  _invocation  _log               _sitecheck  tmp
_cmdline              _jobmode     _mrosource         _tags       _uuid
_filelist             journal      SC_RNA_COUNTER_CS  _timestamp  _versions

this has been showing. As you might know, outs is the folder where the bc matrices are created and stored, but it cannot be seen.

Thank you,

[ATpoint]

I mean, power outages are not programming issues. You see that basically the command works for you. If now it doesn't then I cannot help with that. Check that you have enough memory, or just delete everything and start fresh. outs is indeed the folder you need, if it's not there then try again, see if any hardware interruption was the problem.

Answer 1

[ATpoint]

If it finished successfully you find outputs as described https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/overview

If not then remove the output folders and re-run. Poweroutage is not an error, just an unfortunate event. Just rerun.