When running cellranger-atac mkref, running into an error during the check_reference_format step does not properly print the error due to a bug in they way marian-cs attempts to output the error message. In this particular case, the problem was that there were more than 100 PRIMARY_CONTIGS.
cellranger-atac mkref (1.2.0)
Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
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Non-standard genome name detected, building custom reference...
>>> Creating reference for ci_kh_ghostdb_kh2012_ensembl_mt <<<
Creating new reference folder at /reference-genomes/ciona_intestinalis/ciona_intestinalis_kh_ghostdb_ensembl_mt/cell_ranger_atac_mkref/ci_kh_ghostdb_kh2012_ensembl_mt
Copying original fasta file into reference folder... done
Generating samtools index...
done
Generating pyfasta indexes...
Number of contigs: 1272
Total genome size: 115227500
done
Copying original gene annotation file into reference folder... done
Writing TSS and transcripts bed file...
Parsed 44757 unique TSS and 48038 unique transcripts.
done
Generating bwa index (may take over an hour for a 3Gb genome)...
[bwa_index] Pack FASTA... 0.74 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=230455000, availableWord=28215648
[BWTIncConstructFromPacked] 10 iterations done. 46542904 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 85983976 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 121035288 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 152184952 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 179866808 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 204466488 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 226326712 characters processed.
[bwt_gen] Finished constructing BWT in 73 iterations.
[bwa_index] 42.33 seconds elapse.
[bwa_index] Update BWT... 0.55 sec
[bwa_index] Pack forward-only FASTA... 0.41 sec
[bwa_index] Construct SA from BWT and Occ... 20.21 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /reference-genomes/ciona_intestinalis/ciona_intestinalis_kh_ghostdb_ensembl_mt/cell_ranger_atac_mkref/ci_kh_ghostdb_kh2012_ensembl_mt/fasta/genome.fa
[main] Real time: 64.742 sec; CPU: 64.243 sec
done
Downloading pfm files from source...
done
Finishing up...
Traceback (most recent call last):
File "/opt/cellranger-atac-1.2.0/cellranger-atac-cs/1.2.0/bin/mkref", line 68, in <module>
main()
File "/opt/cellranger-atac-1.2.0/cellranger-atac-cs/1.2.0/bin/mkref", line 62, in main
reference_builder.build_reference()
File "/opt/cellranger-atac-1.2.0/cellranger-atac-cs/1.2.0/lib/python/reference.py", line 548, in build_reference
check_reference_format(self.ref_path)
File "/opt/cellranger-atac-1.2.0/cellranger-atac-cs/1.2.0/lib/python/preflights.py", line 200, in check_reference_format
martian.exit(error_msg)
File "/opt/cellranger-atac-1.2.0/martian-cs/v3.2.4/adapters/python/martian.py", line 265, in exit
_INSTANCE.metadata.write_assert(message)
AttributeError: 'NoneType' object has no attribute 'metadata'
When running
cellranger-atac mkref, running into an error during thecheck_reference_formatstep does not properly print the error due to a bug in they way marian-cs attempts to output the error message. In this particular case, the problem was that there were more than 100 PRIMARY_CONTIGS.