ondisc_matrix has 0 rows or columns; cannot extract sub-matrix into memory

[ggolczer]

Hi Tim,

I am having some trouble with the Nextflow pipeline, I am getting diffent genes and gRNA groups failing precomputations every time (a different one) with the same error "ondisc_matrix has 0 rows or columns; cannot extract sub-matrix into memory." .

Any help with this will be appreciated.

N E X T F L O W ~ version 22.10.6 Launching /home/ubuntu/sceptre-pipeline/main.nf [suspicious_poisson] DSL2 - revision: b0cd4d6075 executor > local (98) executor > local (98) [2b/48fb6c] process > check_inputs [100%] 1 of 1 ✔ [dd/65e4fa] process > perform_gene_precomputation (60) [ 3%] 6 of 189, failed: 6 [93/1d9dc0] process > perform_grna_precomputation (4) [ 0%] 0 of 45 [- ] process > join_gene_precomputations - [- ] process > join_grna_precomputations - [- ] process > perform_pairwise_association_test - [- ] process > combine_results - Error executing process > 'perform_gene_precomputation (47)'

Caused by: Process perform_gene_precomputation (47) terminated with an error exit status (1)

Command executed:

perform_precomputation.R "gene" multimodal_metadata_fp gene_odm_fp gene_to_pod_id_map 47 3 crt

Command exit status: 1

Command output: [1] "Regressing gene ENSG00000111237 onto covariates."

Command error: [1] "Regressing gene ENSG00000111237 onto covariates." Error in extract_matrix(.) : ondisc_matrix has 0 rows or columns; cannot extract sub-matrix into memory. Calls: ... .local -> [[ -> [[ -> .local -> %>% -> extract_matrix Execution halted

Work dir: /data/sceptre_nextflow_top2/work/ad/2d146cb518c1f17239fd08d826c78f

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

[timothy-barry]

Hi Gabriel,I am traveling today and tomorrow, but might you have time for a brief Zoom call? I think this might be easier to sort out verbally!Cheers,TimOn Feb 18, 2023, at 12:00 PM, Gabriel Golczer @.***> wrote: Hi Tim, I am having some trouble with the Nextflow pipeline, I am getting diffent genes and gRNA groups failing precomputations every time (a different one) with the same error "ondisc_matrix has 0 rows or columns; cannot extract sub-matrix into memory." . Any help with this will be appreciated. N E X T F L O W ~ version 22.10.6 Launching /home/ubuntu/sceptre-pipeline/main.nf [suspicious_poisson] DSL2 - revision: b0cd4d6075 executor > local (98) executor > local (98) [2b/48fb6c] process > check_inputs [100%] 1 of 1 ✔ [dd/65e4fa] process > perform_gene_precomputation (60) [ 3%] 6 of 189, failed: 6 [93/1d9dc0] process > perform_grna_precomputation (4) [ 0%] 0 of 45 [- ] process > join_gene_precomputations - [- ] process > join_grna_precomputations - [- ] process > perform_pairwise_association_test - [- ] process > combine_results - Error executing process > 'perform_gene_precomputation (47)' Caused by: Process perform_gene_precomputation (47) terminated with an error exit status (1) Command executed: perform_precomputation.R "gene" multimodal_metadata_fp gene_odm_fp gene_to_pod_id_map 47 3 crt Command exit status: 1 Command output: [1] "Regressing gene ENSG00000111237 onto covariates." Command error: [1] "Regressing gene ENSG00000111237 onto covariates." Error in extract_matrix(.) : ondisc_matrix has 0 rows or columns; cannot extract sub-matrix into memory. Calls: ... .local -> [[ -> [[ -> .local -> %>% -> extract_matrix Execution halted Work dir: /data/sceptre_nextflow_top2/work/ad/2d146cb518c1f17239fd08d826c78f Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: @.***>

[ggolczer]

Sure Tim, my e-mail is golczer@camp4tx.com , we can set up a zoom meeting.

[ggolczer]

Hi Tim, just a nudge here to set up that zoom meeting. We want to submit a publication soon with this data and getting the SCEPTRE Nextflow pipeline to work fully will be a huge help.