CellRanger-ARC for Arbidosis failed with error

[nilesh-iiita]

I am running CellRanger-ARC for Arabidopsis and I am getting the following error:

2023-06-02 14:40:02 [runtime] (failed)          ID.D3.SC_ATAC_GEX_COUNTER_CS.SC_ATAC_GEX_COUNTER._SC_ATAC_GEX_ANALYZER._PEAK_ANNOTATOR.ANNOTATE_PEAKS

[error] Pipestance failed. Error log at:
D3/SC_ATAC_GEX_COUNTER_CS/SC_ATAC_GEX_COUNTER/_SC_ATAC_GEX_ANALYZER/_PEAK_ANNOTATOR/ANNOTATE_PEAKS/fork0/join-uc5dd7a4574/_errors

Log message:
Traceback (most recent call last):
File "/data/rc/apps/rc/software/CellRanger-ARC/2.0.0/external/martian/adapters/python/martian_shell.py", line 659, in _main
stage.main()
File "/data/rc/apps/rc/software/CellRanger-ARC/2.0.0/external/martian/adapters/python/martian_shell.py", line 629, in main
lambda: self._module.join(args, outs, chunk_defs, chunk_outs)
File "/data/rc/apps/rc/software/CellRanger-ARC/2.0.0/external/martian/adapters/python/martian_shell.py", line 589, in _run
cmd()
File "/data/rc/apps/rc/software/CellRanger-ARC/2.0.0/external/martian/adapters/python/martian_shell.py", line 629, in <lambda>
lambda: self._module.join(args, outs, chunk_defs, chunk_outs)
File "/data/rc/apps/rc/software/CellRanger-ARC/2.0.0/mro/atac/stages/analysis/annotate_peaks/init.py", line 105, in join
gene_id_name_map = build_gene_id_name_map(ref_mgr)
File "/data/rc/apps/rc/software/CellRanger-ARC/2.0.0/mro/atac/stages/analysis/annotate_peaks/init.py", line 60, in build_gene_id_name_map
fields.attrs.get("gene_name", fields.attrs["gene_id"])
File "pybedtools/cbedtools.pyx", line 392, in pybedtools.cbedtools.Interval.attrs.get
File "pybedtools/cbedtools.pyx", line 180, in pybedtools.cbedtools.Attributes.init
ValueError: need more than 1 value to unpack

I have tried the following to resolve the issue:

I have updated CellRanger-ARC to the latest version.
I have checked the input data to make sure that it is in the correct format.
I have checked the software used to run CellRanger-ARC to make sure that it is up to date and that it has all of the necessary dependencies.
I am still unable to resolve the issue.

Please help me to troubleshoot this issue.

Thank you.

[RosaDeSa]

I have the same error. Did you solve it?

[Yihui-Zhu]

We have saw this error ValueError: need more than 1 value to unpack before, this error is usually related with GTF format.

Some formatting tips to use:

• retain only gene_id & transcript_id attributes (#can include gene_names if needed)
• replace/remove the empty gene_id entries
• duplicate transcripts_ids for multiple gene_ids have to be converted as unique
• Remove semi colons after gene_name and avoid bloated col9 in the GTF (extraneous information in this col can cause parsing issues)
  More details can be found on our support site: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/advanced/references.

We have high successful rate using Ensembl reference. Here is the link for reference http://ftp.ebi.ac.uk/ensemblgenomes/pub/release-51/plants/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz
http://ftp.ebi.ac.uk/ensemblgenomes/pub/release-51/plants/gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.51.gtf.gz
If there are more questions, feel free to email us at support@10xgenomics.com

[RosaDeSa]

Thanks for the answer, actually I’m working on human data not Arabidopsis and I’m using cellranger arc reference hg38. I’ve this error: File "/opt/cellranger-arc-2.0.2/external/martian/adapters/python/martian_shell.py", line 659, in _main stage.main() File "/opt/cellranger-arc-2.0.2/external/martian/adapters/python/martian_shell.py", line 618, in main self._run(lambda: self._module.main(args, outs)) File "/opt/cellranger-arc-2.0.2/external/martian/adapters/python/martian_shell.py", line 589, in _run cmd() File "/opt/cellranger-arc-2.0.2/external/martian/adapters/python/martian_shell.py", line 618, in <lambda> self._run(lambda: self._module.main(args, outs)) File "/opt/cellranger-arc-2.0.2/mro/atac_rna/stages/preflight/arc_counter_preflight/__init__.py", line 114, in main cr_preflight.record_package_versions() File "/opt/cellranger-arc-2.0.2/lib/python/cellranger/preflight.py", line 348, in record_package_versions version = tk_subproc.check_output(cmd) File "/opt/cellranger-arc-2.0.2/lib/python/tenkit/log_subprocess.py", line 76, in check_output return subprocess.check_output(args, *wargs, **kwargs) File "/opt/cellranger-arc-2.0.2/external/anaconda/lib/python3.7/subprocess.py", line 411, in check_output **kwargs).stdout subprocess.CalledProcessError: Command '['python', '-c', 'import numpy; print(numpy.__version__)']' returned non-zero exit status 1.

…

Il giorno 9 giu 2023, alle ore 23:08, Yihui Zhu ***@***.***> ha scritto: We have saw this error ValueError: need more than 1 value to unpack before, this error is usually related with GTF format. Some formatting tips to use: retain only gene_id & transcript_id attributes (#can include gene_names if needed) replace/remove the empty gene_id entries duplicate transcripts_ids for multiple gene_ids have to be converted as unique Remove semi colons after gene_name and avoid bloated col9 in the GTF (extraneous information in this col can cause parsing issues) More details can be found on our support site: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/advanced/references. We have high successful rate using Ensembl reference. Here is the link for reference http://ftp.ebi.ac.uk/ensemblgenomes/pub/release-51/plants/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz http://ftp.ebi.ac.uk/ensemblgenomes/pub/release-51/plants/gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.51.gtf.gz If there are more questions, feel free to email us at ***@***.*** ***@***.***> — Reply to this email directly, view it on GitHub <#220 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APFLK3KWCZL5BLS6GIVWHDDXKOGFJANCNFSM6AAAAAAYYXLSTU>. You are receiving this because you commented.

[Yihui-Zhu]

For human, we have our prebuild reference here: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/downloads/latest. The build step is here: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/release-notes/references#GRCh38-2020-A-2.0.0. Feel free to send us an email, so we can help more on your specific case.

[RosaDeSa]

I used the recommended reference "refdata-cellranger-arc-GRCh38-2020-A-2.0.0.tar.gz."
My error is the following:

Log message: Traceback (most recent call last): File "/opt/cellranger-arc-2.0.2/external/martian/adapters/python/martian_shell.py", line 659, in _main stage.main() File "/opt/cellranger-arc-2.0.2/external/martian/adapters/python/martian_shell.py", line 618, in main self._run(lambda: self._module.main(args, outs)) File "/opt/cellranger-arc-2.0.2/external/martian/adapters/python/martian_shell.py", line 589, in _run cmd() File "/opt/cellranger-arc-2.0.2/external/martian/adapters/python/martian_shell.py", line 618, in <lambda> self._run(lambda: self._module.main(args, outs)) File "/opt/cellranger-arc-2.0.2/mro/atac_rna/stages/preflight/arc_counter_preflight/__init__.py", line 114, in main cr_preflight.record_package_versions() File "/opt/cellranger-arc-2.0.2/lib/python/cellranger/preflight.py", line 348, in record_package_versions version = tk_subproc.check_output(cmd) File "/opt/cellranger-arc-2.0.2/lib/python/tenkit/log_subprocess.py", line 76, in check_output return subprocess.check_output(args, *wargs, **kwargs) File "/opt/cellranger-arc-2.0.2/external/anaconda/lib/python3.7/subprocess.py", line 411, in check_output **kwargs).stdout File "/opt/cellranger-arc-2.0.2/external/anaconda/lib/python3.7/subprocess.py", line 512, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['python', '-c', 'import numpy; print(numpy.__version__)']' returned non-zero exit status 1.

[nilesh-iiita]

The Gene name in Arabidopsis is inappropriate, so I replaced each gene/symbol name with AGI IDs, and it worked! Using AGI IDs can help ensure consistency and accuracy when working with gene names in Arabidopsis.

[nilesh-iiita]

I have the same error. Did you solve it?

#220 (comment)

[Yihui-Zhu]

Hi @RosaDeSa, since your case is human, this is a different case, please email us at support@10xgenomics.com, so we can help you on your case. Thanks!

[elehnert10x]

Thank you for your interest in Cell Ranger. GitHub Issues are not monitored by our support team. Please e-mail support@10xgenomics.com for support with Cell Ranger or visit our documentation site at https://www.10xgenomics.com/support/software/cell-ranger.