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aertslab / SCENICprotocol

A scalable SCENIC workflow for single-cell gene regulatory network analysis
GNU General Public License v3.0
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nextflow Segmentation fault preprocess_visualize_project_scanpy.py cluster #82

Open vagabond12 opened 7 months ago

vagabond12 commented 7 months ago

(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: 37e555c112 [master]

Project name: SCENIC Protocol Project dir : /home/ahmu/.nextflow/assets/aertslab/SCENICprotocol Git info: https://github.com/aertslab/SCENICprotocol - master [37e555c112cc4f55a26ef3f7c232ffe9238ae476] 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_20190621ChIP_seq_transcription_factor.hg38refseq-r8010kb_up_and_down_tss.max.genes_vs_tracks.rankings.feather /home/soft/scenicDB/hg38/encode_20190621ChIP_seq_transcription_factor.hg38refseq-r80500bp_up_and_100bp_down_tss.max.genes_vs_tracks.rankings.feather /home/soft/scenicDB/hg38/hg38refseq-r8010kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather /home/soft/scenicDB/hg38/hg38refseq-r80500bp_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?