Error: Pipestance failed

[pierovatti]

Hi, I've been trying to run snpclust on my single cell data.

After installing all the depencies, I created a .mro file, setting the reference_path to the directory containing my reference data (refdata-cellranger-hg19-1.2.0), and the possorted_genome_bam and cell_barcodes variables to the bam and barcodes file of one of my samples.

Then I run a bash script setting the PATH variables and giving the command
ranger mrp example.mro example

However, I receive this message:

ranger mrp (1.0.1)
Copyright (c) 2016 10x Genomics, Inc.  All rights reserved.
-------------------------------------------------------------------------------

Martian Runtime - 1.0.1 (2.1.2)
2022-06-21 14:13:08 [runtime] Reattaching in local mode.
2022-06-21 14:13:08 [runtime] (reset-partial)   ID.example.SNP_CLUSTERER_CS.SNP_CLUSTERER.FILTER_READS.fork0.split
2022-06-21 14:13:08 [runtime] (ready)           ID.example.SNP_CLUSTERER_CS.SNP_CLUSTERER.FILTER_READS
2022-06-21 14:13:08 [runtime] (run:local)       ID.example.SNP_CLUSTERER_CS.SNP_CLUSTERER.FILTER_READS.fork0.split
2022-06-21 14:13:11 [runtime] (failed)          ID.example.SNP_CLUSTERER_CS.SNP_CLUSTERER.FILTER_READS

[error] Pipestance failed. Please see log at:
example/SNP_CLUSTERER_CS/SNP_CLUSTERER/FILTER_READS/fork0/split/_errors

Looking at the error file, this is what it says:

Traceback (most recent call last):
  File "/opt/common/tools/ric.vago/10x/ranger-1.0.1/martian-cs/2.1.2/adapters/python/split.py", line 13, in <module>
    martian.initialize(sys.argv)
  File "/opt/common/tools/ric.vago/10x/ranger-1.0.1/martian-cs/2.1.2/adapters/python/martian.py", line 354, in initialize
    module = __import__(os.path.basename(stagecode_path))
  File "/opt/common/tools/ric.vago/10x/single-cell-3prime-snp-clustering-master/mro/stages/snpclust/filter_reads/__init__.py", line 7, in <module>
    import cellranger.constants as cr_constants
ImportError: No module named cellranger.constants

I'm quite new to coding and analyzing single cell data, so I don't know what to do without messing up everything.
Have you encountered this problem in the past? Is there a way to solve this?

Also, I don't know if it helps but I'm using cellranger-6.0.1