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AberrantSplicing pipeline error
I was running the drop demo as like this
drop demo snakemake aberrantExpression --cores 30
But it got error like this
Finished job 13. 16 of 69 steps (23%) done Loading required package: rtracklayer Loading required package: rtracklayer Loading required package: rtracklayer Loading required package: rtracklayer Loading required package: rtracklayer Wed Jan 10 14:53:11 2024: Count split reads for sample: HG00150 Wed Jan 10 14:53:11 2024: Count split reads for sample: HG00111 Wed Jan 10 14:53:11 2024: Count split reads for sample: HG00096 Wed Jan 10 14:53:12 2024: Count split reads for sample: HG00106 Wed Jan 10 14:53:12 2024: Count split reads for sample: HG00132 Loading required package: rtracklayer Wed Jan 10 14:53:13 2024: Count split reads for sample: HG00126 Error in find_NCBI_assembly_ftp_dir(assembly_accession, assembly_name = assembly_name) : unable to find FTP dir for assembly GCF_000001405.25 in https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/ Calls: countSplitReads ... .form_assembly_report_url -> find_NCBI_assembly_ftp_dir Execution halted [Wed Jan 10 14:53:15 2024] Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R: jobid: 20 input: testRNA/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/fds.done, Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R output: testRNA/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser/sample_tmp/splitCounts/sample_HG00096.done log: testRNA/drop_demo/.drop/tmp/AS/fraser/splitReads/HG00096.Rds (check log file(s) for error details)
RuleException: CalledProcessError in file /local/a992a/23555406/cluster_tmp/tmpv8rlvb_b, line 130: Command 'set -euo pipefail; Rscript --vanilla testRNA/drop_demo/.snakemake/scripts/tmpso0ytzon.01_1_countRNA_splitReads_samplewise.R' returned non-zero exit status 1. File "/local/a992a/23555406/cluster_tmp/tmpv8rlvb_b", line 130, in __rule_AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R File "/home/a992a/micromamba/envs/drop_env_133/lib/python3.8/concurrent/futures/thread.py", line 57, in run Loading required package: rtracklayer Loading required package: rtracklayer Wed Jan 10 14:53:17 2024: Count split reads for sample: HG00149 Wed Jan 10 14:53:17 2024: fraser_external, HG00150 no. splice junctions (split counts) = 472 Wed Jan 10 14:53:17 2024: fraser_external, HG00132 no. splice junctions (split counts) = 469 Wed Jan 10 14:53:17 2024: Count split reads for sample: HG00176 [Wed Jan 10 14:53:17 2024] Finished job 42. 17 of 69 steps (25%) done Wed Jan 10 14:53:17 2024: fraser_external, HG00111 no. splice junctions (split counts) = 468 [Wed Jan 10 14:53:17 2024] Finished job 43. 18 of 69 steps (26%) done [Wed Jan 10 14:53:18 2024] Finished job 40. 19 of 69 steps (28%) done Wed Jan 10 14:53:18 2024: fraser_external, HG00126 no. splice junctions (split counts) = 511 Wed Jan 10 14:53:18 2024: fraser_external, HG00106 no. splice junctions (split counts) = 500 [Wed Jan 10 14:53:18 2024] Finished job 41. 20 of 69 steps (29%) done [Wed Jan 10 14:53:18 2024] Finished job 45. 21 of 69 steps (30%) done Wed Jan 10 14:53:22 2024: fraser_external, HG00176 no. splice junctions (split counts) = 469 [Wed Jan 10 14:53:22 2024] Finished job 46. 22 of 69 steps (32%) done Wed Jan 10 14:53:23 2024: fraser_external, HG00149 no. splice junctions (split counts) = 523 [Wed Jan 10 14:53:23 2024] Finished job 44. 23 of 69 steps (33%) done Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message
Rest pipelines like aberrantExpression and mae running with out any error
What will be the reason for this error ?
Hi, can you share the parameters of your config file? The global ones and the aberrantSplicing ones
projectTitle: Detection of RNA Outlier Pipeline htmlOutputPath: testRNA/drop_demo/Output/html indexWithFolderName: true root:testRNA/drop_demo/Output sampleAnnotation: testRNA/drop_demo/Data/sample_annotation.tsv geneAnnotation: v29: testRNA/drop_demo/Data/gencode_annotation_trunc.gtf genomeAssembly: hg19 genome: ncbi: testRNA/drop_demo/Data/chr21_ncbi.fa ucsc: testRNA/drop_demo/Data/chr21.fa hpoFile: null random_seed: true exportCounts: geneAnnotations:
- v29 excludeGroups:
- mae
- outrider_external
- fraser_external tools: gatkCmd: gatk bcftoolsCmd: bcftools samtoolsCmd: samtools
aberrantSplicing: run: true groups:
- fraser
- fraser_external recount: true longRead: false keepNonStandardChrs: false filter: false minExpressionInOneSample: 20 quantileMinExpression: 10 quantileForFiltering: 0.95 minDeltaPsi: 0.05 implementation: PCA padjCutoff: 1 maxTestedDimensionProportion: 6 genesToTest: Data/genes_to_test.yaml FRASER_version: FRASER deltaPsiCutoff: 0.05
Hi, hard to say, could be that the ncbi webpage was not working on that day. Otherwise, can you change your genomeAssembly param from hg19 to GRCh37?
Hi, were you able to rerun the pipeline?