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gagneurlab / drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
MIT License
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Error in MAE QC create matrix dna rna cor #527

Closed bijuissac closed 2 months ago

bijuissac commented 3 months ago

Hi

I keep getting error at the create matrix step. Based on error described below, it seems to be parallel job errors. However I am not sure. Does anyone have any clue to correct this?

`rule MonoallelicExpression_pipeline_QC_create_matrix_dna_rna_cor_R: input: /hpcdata/bcbb/bissac/Clinical_Genomics/Projects/Helen_Su/results/drop_results/DROP_pipeline_monoallelicExpression_MAE2/Output/processed_data/mae/RNA_GT/2491270_JCC454_37.Rds, /hpcdata/bcbb/bi ssac/Clinical_Genomics/Projects/Helen_Su/results/drop_results/DROP_pipeline_monoallelicExpression_MAE2/Output/processed_data/mae/RNA_GT/2491263_JCC454_9.Rds, /hpcdata/bcbb/bissac/Clinical_Genomics/Proje cts/Helen_Su/results/drop_results/DROP_pipeline_monoallelicExpression_MAE2/Output/processed_data/mae/RNA_GT/2491261_JCC454_1.Rds, /hpcdata/bcbb/bissac/Clinical_Genomics/Projects/Helen_Su/results/drop_re sults/DROP_pipeline_monoallelicExpression_MAE2/Output/processed_data/mae/RNA_GT/2491266_JCC454_21.Rds, /hpcdata/bcbb/bissac/Clinical_Genomics/Projects/Helen_Su/results/drop_results/DROP_pipeline_monoall elicExpression_MAE2/Output/processed_data/mae/RNA_GT/2491271_JCC454_41.Rds, /hpcdata/bcbb/bissac/Clinical_Genomics/Projects/Helen_Su/results/drop_results/DROP_pipeline_monoallelicExpression_MAE2/Output/ processed_data/mae/RNA_GT/2491267_JCC454_25.Rds, /hpcdata/bcbb/bissac/Clinical_Genomics/Projects/Helen_Su/results/drop_results/DROP_pipeline_monoallelicExpression_MAE2/Output/processed_data/mae/RNA_GT/2 491264_JCC454_13.Rds, /hpcdata/bcbb/bissac/Clinical_Genomics/Projects/Helen_Su/results/drop_results/DROP_pipeline_monoallelicExpression_MAE2/Output/processed_data/mae/RNA_GT/2491269_JCC454_33.Rds, /hpcd ata/bcbb/bissac/Clinical_Genomics/Projects/Helen_Su/results/drop_results/DROP_pipeline_monoallelicExpression_MAE2/Output/processed_data/mae/RNA_GT/2491268_JCC454_29.Rds, /hpcdata/bcbb/bissac/Clinical_Ge nomics/Projects/Helen_Su/results/drop_results/DROP_pipeline_monoallelicExpression_MAE2/Output/processed_data/mae/RNA_GT/2491265_JCC454_17.Rds, Scripts/MonoallelicExpression/pipeline/QC/create_matrix_dna _rna_cor.R output: /hpcdata/bcbb/bissac/Clinical_Genomics/Projects/Helen_Su/results/drop_results/DROP_pipeline_monoallelicExpression_MAE2/Output/processed_results/mae/mae/dna_rna_qc_matrix.Rds log: /hpcdata/bcbb/bissac/Clinical_Genomics/Projects/Helen_Su/results/drop_results/DROP_pipeline_monoallelicExpression_MAE2/.drop/tmp/MAE/mae/QC_matrix.Rds jobid: 0 reason: Forced execution wildcards: dataset=mae threads: 20 resources: mem_mb=1000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/hpcdata/scratch/24734494.1.all.q

Stop worker failed with the error: reached CPU time limit Error: BiocParallel errors 0 remote errors, element index: 10 unevaluated and other errors first remote error: Execution halted `

vyepez88 commented 2 months ago

Hi, the reason seems to be this: reached CPU time limit Is there a way you can allocate more resources? 1 Gb is not a lot.

bijuissac commented 2 months ago

Hi, sorry for not coming back to close this. We resolved the error. Digging deeper, we found out that the QC VCF and the sample data data VCF header had different assembly names (38 and hg38). The script proceeded to complete successfully once this was rectified in the headers of both VCFs to match. We did try increasing resources (our thoughts initially) but it did not help

bijuissac commented 2 months ago

Resolved