Troubleshooting

Below is a list of known issues you may encounter when running spacemake. As spacemake depends on several external libraries and tools, it is not always possible to resolve some of these issues.

Bumped on another problem which is not documented here? Feel free to open an issue on Github.

GLIBCXX_xxx not found

In certain environments you might run into the following error:

ImportError: /lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /.../envs/spacemake/lib/python3.10/site-packages/matplotlib/_path.cpython-310-x86_64-linux-gnu.so)

Certain dependencies (e.g. scipy) might affect this. To overcome it, try the following:

export LD_LIBRARY_PATH=/conda_installation_folder/envs/spacemake/lib:$LD_LIBRARY_PATH

For more details on this and further troubleshooting visit stackoverflow.

Issues with memory usage

Certain steps of the spacemake workflow might currently result in excessive memory usage. These occur in samples where a large number of barcodes exist in the data, such as for stero-seq or open-ST. The excessive memory usage is due to using the Drop-seq tools, where a specific memory size is allocated for java.

We are working on removing the depndency to the Drop-seq tools altogether, which will also speed up several steps. If you run into memory errors, however, you can solve them by modifying the main.smk file inside your spacemake installation, which should be somewhere in

/path_to_conda/envs/spacemake/lib/python3.10/site-packages/spacemake/snakemake

inside your conda installation folder. Simply modify the following lines

{dropseq_tools}/BamTagHistogram -m 32g
{dropseq_tools}/DigitalExpression -m 16g

by increasing the value of -m accordingly.

Issues with STAR

To reduce memory usage when running several samples at the same time, spacemake uses STAR’s shared memory capability. This currently has the following limitations:

  1. It is not possible for one user to run two distinct spacemake instances with the same genome index. Multiple spacemake instances (each processing several samples) can run at the same time if different species indexes are used.

  2. Similarly, it is not possible that two users can run spacemake with the same genome index loaded at the same time.

In addition to the above, you might run into STAR-related errors if the spacemake instance was killed before finishing. This occurs when the genome index is still loaded into memory, and STAR will either throw an error and exit, or just stall. In that case, try to run:

STAR --genomeLoad Remove --genomeDir <genome_dir>

In case the shared memory cannot be released (Linux), try the following:

ipcs -m | grep `whoami` | awk '{ print $2 }' | xargs -n1 ipcrm -m