GraffiTE exiting at minimap due to "Unknown option: --no-home"

[jamesdgalbraith]

I've been trying to run GraffiTE on a cluster and am having it fail at the alignment step. Do you have any pointers on how I can getting it running? I'm not sure if this is a bug with Nextflow/Singularity or with GraffiTE.

Here's the command I've used with the test data, and the log output below

nextflow run /ceph/users/jgalbraith/Programs/GraffiTE/main.nf \
   --reference hs37d5.chr22.fa --assemblies assemblies.csv --reads reads.csv --TE_library human_DFAM3.6.fasta \
   --cores 40 -with-singularity /ceph/users/jgalbraith/Programs/GraffiTE/graffite_latest.sif

N E X T F L O W  ~  version 23.10.1
Launching `/ceph/users/jgalbraith/Programs/GraffiTE/main.nf` [fabulous_mccarthy] DSL2 - revision: 20270181eb


▄████  ██▀███   ▄▄▄        █████▒ █████▒██▓▄▄▄█████▓▓█████
██▒ ▀█▒▓██ ▒ ██▒▒████▄    ▓██   ▒▓██           ██▒ ▓▒▓█   ▀
▒██░▄▄▄░▓██ ░▄█ ▒▒██  ▀█▄  ▒████ ░▒████ ░▒██▒▒ ▓██░ ▒░▒███
░▓█  ██▓▒██▀▀█▄  ░██▄▄▄▄██ ░▓█▒  ░░▓█▒  ░░██░░ ▓██▓ ░ ▒▓█  ▄
░▒▓███▀▒░██▓ ▒██▒  █   ▓██▒░▒█░   ░▒█░   ░██░  ▒██▒ ░ ░▒████▒
░▒   ▒ ░ ▒▓ ░▒▓░ ▒▒   ▓▒█░ ▒ ░    ▒ ░   ░▓    ▒ ░░   ░░ ▒░ ░
░   ░   ░▒ ░ ▒░  ▒   ▒▒ ░ ░      ░      ▒ ░    ░     ░ ░  ░
░ ░   ░   ░░   ░   ░   ▒    ░ ░    ░ ░    ▒ ░  ░         ░
░    ░           ░  ░               ░              ░  ░

V . null

Find and Genotype Transposable Elements Insertion Polymorphisms
in Genome Assemblies using a Pangenomic Approach

Authors: Cristian Groza and Clément Goubert
Bug/issues: https://github.com/cgroza/GraffiTE/issues


[-        ] process > map_asm        -
[-        ] process > svim_asm       -
[-        ] process > survivor_merge -
[-        ] process > repeatmask_VCF -
[-        ] process > tsd_prep       -
[-        ] process > tsd_search     -
[-        ] process > tsd_report     -
[-        ] process > pangenie       -
[-        ] process > merge_VCFs     -

executor >  local (1)
[ef/f8e87c] process > map_asm (1)    [  0%] 0 of 1
[-        ] process > svim_asm       -
[-        ] process > survivor_merge -
[-        ] process > repeatmask_VCF -
[-        ] process > tsd_prep       -
[-        ] process > tsd_search     -
[-        ] process > tsd_report     -
[-        ] process > pangenie       -
[-        ] process > merge_VCFs     -

executor >  local (1)
[ef/f8e87c] process > map_asm (1)    [  0%] 0 of 1
[-        ] process > svim_asm       -
[-        ] process > survivor_merge -
[-        ] process > repeatmask_VCF -
[-        ] process > tsd_prep       -
[-        ] process > tsd_search     -
[-        ] process > tsd_report     -
[-        ] process > pangenie       -
[-        ] process > merge_VCFs     -
ERROR ~ Error executing process > 'map_asm (1)'

Caused by:
  Process `map_asm (1)` terminated with an error exit status (1)

Command executed:

  minimap2 -a -x asm5 --cs -r2k -t 40 -K 500M hs37d5.chr22.fa HG002.mat.cur.20211005_chr22.fasta.gz | samtools sort -m4G -@4 -o asm.sorted.bam -

Command exit status:
  1

Command output:
  (B

Command error:
  ERROR: Unknown option: --no-home
  (B

Work dir:
  /ceph/users/jgalbraith/Programs/GraffiTE/test/GraffiTE_testset/work/ef/f8e87c34a7cc24ce498d825f4b43f8

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details

executor >  local (1)
[ef/f8e87c] process > map_asm (1)    [100%] 1 of 1, failed: 1 ✘
[-        ] process > svim_asm       -
[-        ] process > survivor_merge -
[-        ] process > repeatmask_VCF -
[-        ] process > tsd_prep       -
[-        ] process > tsd_search     -
[-        ] process > tsd_report     -
[-        ] process > pangenie       -
[-        ] process > merge_VCFs     -
ERROR ~ Error executing process > 'map_asm (1)'

Caused by:
  Process `map_asm (1)` terminated with an error exit status (1)

Command executed:

  minimap2 -a -x asm5 --cs -r2k -t 40 -K 500M hs37d5.chr22.fa HG002.mat.cur.20211005_chr22.fasta.gz | samtools sort -m4G -@4 -o asm.sorted.bam -

Command exit status:
  1

Command output:
  (B

Command error:
  ERROR: Unknown option: --no-home
  (B

Work dir:
  /ceph/users/jgalbraith/Programs/GraffiTE/test/GraffiTE_testset/work/ef/f8e87c34a7cc24ce498d825f4b43f8

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details