AberrantSplicing pipeline error

[akhilvelluva]

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 ?

[vyepez88]

Hi, can you share the parameters of your config file? The global ones and the aberrantSplicing ones

[akhilvelluva]

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

[vyepez88]

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?

[vyepez88]

Hi, were you able to rerun the pipeline?