Version: Cellranger v4.0.0
Hi,
I use cellranger mkref to build the customized mm10 genome reference. But it always showes error like this:
May 03 20:17:47 ..... Started STAR run
['/home/panyiru/software/cellranger-4.0.0/bin/rna/mkref', '--genome=mm10', '--nthreads=20', '--fasta=Mus_musculus.GRCm39.dna.toplevel.fa', '--genes=Mus_musculus.GRCm39.106.filtered.gtf', '--ref-version=4.0.0']
Creating new reference folder at /home/panyiru/sc/mouse/mm10
...done
Writing genome FASTA file into reference folder...
...done
Computing hash of genome FASTA file...
...done
Indexing genome FASTA file...
...done
Writing genes GTF file into reference folder...
...done
Computing hash of genes GTF file...
...done
Writing genes index file into reference folder (may take over 10 minutes for a 3Gb genome)...
...done
Writing genome metadata JSON file into reference folder...
...done
Generating STAR genome index (may take over 8 core hours for a 3Gb genome)...
Traceback (most recent call last):
File "/home/panyiru/software/cellranger-4.0.0/bin/rna/mkref", line 108, in <module>
main()
File "/home/panyiru/software/cellranger-4.0.0/bin/rna/mkref", line 105, in main
referenceBuilder.build_reference()
File "/home/panyiru/software/cellranger-4.0.0/lib/python/cellranger/reference.py", line 410, in build_reference
new_genome_fasta, new_gene_gtf, num_threads=self.num_threads, mem_gb=self.mem_gb
File "/home/panyiru/software/cellranger-4.0.0/lib/python/cellranger/reference.py", line 787, in index_reference_with_mem_gb
limit_ram=limit_ram,
File "/home/panyiru/software/cellranger-4.0.0/lib/python/cellranger/reference.py", line 827, in index_reference
tk_subproc.check_call(args)
File "/home/panyiru/software/cellranger-4.0.0/lib/python/tenkit/log_subprocess.py", line 43, in check_call
return subprocess.check_call(*args, **kwargs)
File "/home/panyiru/software/cellranger-4.0.0/external/anaconda/lib/python2.7/subprocess.py", line 190, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['STAR', '--runMode', 'genomeGenerate', '--genomeDir', '/home/panyiru/sc/mouse/mm10/star', '--runThreadN', '20', '--genomeFastaFiles', '/home/panyiru/sc/mouse/mm10/fasta/genome.fa', '--sjdbGTFfile', '/home/panyiru/sc/mouse/mm10/genes/genes.gtf', '--limitGenomeGenerateRAM', '17179869184', '--genomeSAsparseD', '3', '--genomeSAindexNbases', '14', '--genomeChrBinNbits', '18']' returned non-zero exit status -4
I tried to find the same question from other people, I found there is a same question: https://www.biostars.org/p/394710/. But I tried to use --memgb=64, it didn't work.
At the same time, I try running it without the --nthreads option in the suggestion with 10x official, but it doesn't work.
Can anybody tell me what is wrong with this?
Thanks, Yuri
Version: Cellranger v4.0.0 Hi, I use cellranger mkref to build the customized mm10 genome reference. But it always showes error like this:
I tried to find the same question from other people, I found there is a same question: https://www.biostars.org/p/394710/. But I tried to use --memgb=64, it didn't work. At the same time, I try running it without the --nthreads option in the suggestion with 10x official, but it doesn't work. Can anybody tell me what is wrong with this? Thanks, Yuri