nextflow Segmentation fault preprocess_visualize_project_scanpy.py cluster

[vagabond12]

(base) [ahmu@AMD demo]$ nextflow run aertslab/SCENICprotocol -profile singularity --loom_input /home/ahmu/demo/CS78-EPI5718.loom --loom_output pyscenic_integrated-output.loom --TFs /home/soft/scenicDB/allTFs_hg38.txt --motifs /home/soft/scenicDB/motifs-v9-nr.hgnc-m0.001-o0.0.tbl --db "/home/soft/scenicDB/hg38/*feather" --pyscenic_container=/home/soft/aertslab-pyscenic-scanpy-0.12.1-1.9.1.sif --seed 777
N E X T F L O W ~ version 21.04.3
Launching aertslab/SCENICprotocol [curious_venter] - revision: 37e555c [master]

---

Project name: SCENIC Protocol
Project dir : /home/ahmu/.nextflow/assets/aertslab/SCENICprotocol
Git info: https://github.com/aertslab/SCENICprotocol - master [37e555c]
Cmd line: nextflow run aertslab/SCENICprotocol -profile singularity --loom_input /home/ahmu/demo/CS78-EPI5718.loom --loom_output pyscenic_integrated-output.loom --TFs /home/soft/scenicDB/allTFs_hg38.txt --motifs /home/soft/scenicDB/motifs-v9-nr.hgnc-m0.001-o0.0.tbl --db '/home/soft/scenicDB/hg38/*feather' --pyscenic_container=/home/soft/aertslab-pyscenic-scanpy-0.12.1-1.9.1.sif --seed 777
Pipeline version: 0.2.0

---

Parameters in use:
loom_input=/home/ahmu/demo/CS78-EPI5718.loom
loom_filtered=filtered.loom
loom_output=pyscenic_integrated-output.loom
thr_min_genes=200
thr_min_cells=3
thr_n_genes=5000
thr_pct_mito=0.25
outdir=output
threads=6
TFs=/home/soft/scenicDB/allTFs_hg38.txt
motifs=/home/soft/scenicDB/motifs-v9-nr.hgnc-m0.001-o0.0.tbl
db=/home/soft/scenicDB/hg38/*feather
pyscenic_output=pyscenic_output.loom
grn=grnboost2
cell_id_attribute=CellID
gene_attribute=Gene
pyscenic_container=/home/soft/aertslab-pyscenic-scanpy-0.12.1-1.9.1.sif
seed=777

---

Using 4 feather databases:
/home/soft/scenicDB/hg38/encode_20190621__ChIP_seq_transcription_factor.hg38__refseq-r80__10kb_up_and_down_tss.max.genes_vs_tracks.rankings.feather
/home/soft/scenicDB/hg38/encode_20190621__ChIP_seq_transcription_factor.hg38__refseq-r80__500bp_up_and_100bp_down_tss.max.genes_vs_tracks.rankings.feather
/home/soft/scenicDB/hg38/hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather
/home/soft/scenicDB/hg38/hg38__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.genes_vs_motifs.rankings.feather

---

executor > local (6)
executor > local (6)
[54/6df470] process > filter [100%] 1 of 1 ✔
[bd/bb1087] process > preprocess [100%] 1 of 1 ✔
[41/8e4082] process > pca [100%] 1 of 1 ✔
[90/f2422d] process > visualize [100%] 1 of 1 ✔
[06/cea557] process > cluster [100%] 1 of 1, failed: 1 ✘
[- ] process > GRNinference -
[- ] process > cisTarget -
[- ] process > AUCell -
[- ] process > visualizeAUC -
[- ] process > integrateOutput -
Error executing process > 'cluster'

Caused by:
Process cluster terminated with an error exit status (139)

Command executed:

preprocess_visualize_project_scanpy.py cluster --anndata anndata.h5ad --threads 6

Command exit status:
139

Command output:
(empty)

Command error:
.command.sh: line 2: 53751 Segmentation fault (core dumped) preprocess_visualize_project_scanpy.py cluster --anndata anndata.h5ad --threads 6

Work dir:
/home/ahmu/demo/work/06/cea55727742997e6b57e705383d05f

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

How to use nextflow with pyscenic-0.12.0 or 0.12.1?