Creating new reference folder at /data/local/rajewsky/home/aantona/custome_genome_mouse_bgh/refdata-gex-mm10-2020-A_bigT_bGH/mm10-2020-A_BigT_bGH
...done
Writing genome FASTA file into reference folder...
...done
Indexing genome FASTA file...
Traceback (most recent call last):
File "/data/local/rajewsky/home/aantona/yard/apps/cellranger-7.0.0/bin/rna/mkref", line 137, in <module>
main()
File "/data/local/rajewsky/home/aantona/yard/apps/cellranger-7.0.0/bin/rna/mkref", line 128, in main
reference_builder.build_gex_reference()
File "/data/local/rajewsky/home/aantona/yard/apps/cellranger-7.0.0/lib/python/cellranger/reference_builder.py", line 209, in build_gex_reference
self.process_fasta()
File "/data/local/rajewsky/home/aantona/yard/apps/cellranger-7.0.0/lib/python/cellranger/reference_builder.py", line 93, in process_fasta
stdout = tk_subproc.check_output(
File "/data/local/rajewsky/home/aantona/yard/apps/cellranger-7.0.0/lib/python/tenkit/log_subprocess.py", line 67, in check_output
return subprocess.check_output(args, *wargs, **kwargs)
File "/data/local/rajewsky/home/aantona/yard/apps/cellranger-7.0.0/external/anaconda/lib/python3.8/subprocess.py", line 415, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/data/local/rajewsky/home/aantona/yard/apps/cellranger-7.0.0/external/anaconda/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/data/local/rajewsky/home/aantona/yard/apps/cellranger-7.0.0/external/anaconda/bin/samtools', 'faidx', '/data/local/rajewsky/home/aantona/custome_genome_mouse_bgh/refdata-gex-mm10-2020-A_bigT_bGH/mm10-2020-A_BigT_bGH/fasta/genome.fa']' returned non-zero exit status 1.
My command is
`cellranger mkref --genome=mm10-2020-A_BigT_bGH --fasta=mm10-2020-A_bigT_bGH.fa --genes=mm10-2020-A_bigT_bGH.gtf --nthreads=64 --memgb=256 .`
and my folderlooks like this after running the cellranger mkref ( it stops when is creating the genome.fa)
Hello,
I am trying to build a custom mouse genome! I use the reference genome and gtf file from 10x and modified as described here: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_mr#panel
My error message is the following
Anna