You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I ran the workflow on the demo dataset provided by this workflow, and I get different results when running --cnv with and without --use_qdnaseq. The reports also look different, with useful graphs present in the version using QDNAseq no longer present with Spectre.
When running with QDNAseq, I get a CNV for chromosome 20, but I get no CNV when running with Spectre on the same demo dataset.
I included the run output for the run with Spectre and the two reports in PDF.
Relevant log output
curl: (28) Failed to connect to www.nextflow.io port 443 after 300100 ms: Timeout was reached
N E X T F L O W ~ version 23.10.0
Launching `https://github.com/epi2me-labs/wf-human-variation` [lonely_saha] DSL2 - revision: 5651930a05 [master]
|||||||||| _____ ____ ___ ____ __ __ _____ _ _
||||||||||| ____| _ \_ _|___ \|\/| ____||| __ _||__ ___
|||||| _|||_) || __) ||\/|| _| _____||/ _`|'_ \/ __|||||| | |___| __/| | / __/| | | | |__|_____| | (_| | |_) \__ \|||||||||| |_____|_| |___|_____|_| |_|_____| |_|\__,_|_.__/|___/|||||||||| wf-human-variation v2.2.0-g5651930--------------------------------------------------------------------------------Core Nextflow options revision : master runName : lonely_saha containerEngine : apptainer container : [withLabel:wf_human_snp:ontresearch/wf-human-variation-snp:sha6d5c80963ce346695d98205563c87dc71fc182ff, withLabel:wf_human_sv:ontresearch/wf-human-variation-sv:sha8f02fbfaea233fe4763f7c7142696efcadab2f4d, withLabel:wf_human_mod:ontresearch/modkit:sha0253e9e9ba92aacc852ba376edefe8ff0932f71a, withLabel:wf_cnv:ontresearch/wf-cnv:sha428cb19e51370020ccf29ec2af4eead44c6a17c2, withLabel:wf_human_str:ontresearch/wf-human-variation-str:shaa2f49ce57886426516eadd4048b6fdf9c22c7437, withLabel:snpeff_annotation:ontresearch/snpeff:sha313729d816872d70b410752001a0e2654eb88807, withLabel:wf_common:ontresearch/wf-common:sha91cd87900c86f05bf36d8c77b841b8fda5ecf3aa, withLabel:spectre:ontresearch/spectre:sha15d6757d00b503344d0b1054473ffeb5e3cab79d, default:ontresearch/wf-human-variation:sha0f033fe23a576cf4da9df8d2d6745d63329a8611] launchDir : /home/clawrukd/wf-human-variation-test workDir : /home/clawrukd/wf-human-variation-test projectDir : /home/clawrukd/.nextflow/assets/epi2me-labs/wf-human-variation userName : clawrukd profile : apptainer configFiles : /home/clawrukd/.nextflow/assets/epi2me-labs/wf-human-variation/nextflow.config, /home/clawrukd/apptainer_nextflow.configWorkflow Options sv : true snp : true cnv : true str : trueMain options sample_name : DEMO bam : /home/clawrukd/wf-human-variation-test/wf-human-variation-demo/demo.bam ref : /home/clawrukd/wf-human-variation-test/wf-human-variation-demo/demo.fasta basecaller_cfg : dna_r10.4.1_e8.2_400bps_hac_prom phased : true out_dir : /home/clawrukd/wf-human-variation-test/SpectreMultiprocessing Options threads : 40 ubam_map_threads: 30!! Only displaying parameters that differ from the pipeline defaults !!--------------------------------------------------------------------------------If you use epi2me-labs/wf-human-variation for your analysis please cite:* The nf-core framework https://doi.org/10.1038/s41587-020-0439-x--------------------------------------------------------------------------------This is epi2me-labs/wf-human-variation v2.2.0-g5651930.--------------------------------------------------------------------------------executor > local (90)[80/732b1d] process > ingress:checkBamHeaders (1) [100%] 1 of 1, cached: 1 ✔[- ] process > ingress:sortBam -[- ] process > ingress:mergeBams -[- ] process > ingress:catSortBams -[35/d5d577] process > ingress:validateIndex (1) [100%] 1 of 1, cached: 1 ✔[- ] process > ingress:samtools_index -[04/9fb071] process > ingress:check_for_alignment... [100%] 1 of 1, cached: 1 ✔[- ] process > ingress:minimap2_alignment -[e0/b38fb9] process > getGenome (1) [100%] 1 of 1 ✔[a2/7ee4f4] process > cram_cache (1) [100%] 1 of 1, cached: 1 ✔[e6/4b2821] process > getAllChromosomesBed (1) [100%] 1 of 1, cached: 1 ✔[5a/7cd542] process > mosdepth_input (1) [100%] 1 of 1, cached: 1 ✔[76/6b440c] process > getVersions [100%] 1 of 1, cached: 1 ✔[57/6f978b] process > getParams [100%] 1 of 1, cached: 1 ✔[9a/78ba5c] process > readStats (1) [100%] 1 of 1, cached: 1 ✔[95/4d56e6] process > infer_sex (1) [100%] 1 of 1, cached: 1 ✔[0f/ef986a] process > makeAlignmentReport [100%] 1 of 1, cached: 1 ✔[- ] process > failedQCReport -[5f/d272f5] process > lookup_clair3_model (1) [100%] 1 of 1, cached: 1 ✔[f2/717b83] process > snp:make_chunks (1) [100%] 1 of 1 ✔[04/f3c28a] process > snp:pileup_variants (6) [100%] 13 of 13 ✔[09/7e6bda] process > snp:aggregate_pileup_varian... [100%] 1 of 1 ✔[eb/d835ea] process > snp:select_het_snps (1) [100%] 1 of 1 ✔[7b/cba70a] process > snp:phase_contig (1) [100%] 1 of 1 ✔[fb/c63951] process > snp:get_qual_filter (1) [100%] 1 of 1 ✔[bb/dbf178] process > snp:create_candidates (1) [100%] 1 of 1 ✔[da/6a76d8] process > snp:evaluate_candidates (2) [100%] 15 of 15 ✔[ec/12613c] process > snp:aggregate_full_align_va... [100%] 1 of 1 ✔[d4/303f2b] process > snp:merge_pileup_and_full_v... [100%] 1 of 1 ✔[b3/755002] process > snp:post_clair_phase_contig... [100%] 1 of 1 ✔[d5/f47238] process > snp:post_clair_contig_haplo... [100%] 1 of 1 ✔[52/b10347] process > snp:cat_haplotagged_contigs... [100%] 1 of 1 ✔[e1/819305] process > snp:aggregate_all_variants (1) [100%] 1 of 1 ✔[1f/fe7f31] process > snp:haploblocks_snp (1) [100%] 1 of 1 ✔[82/ae48f0] process > sv:variantCall:sniffles2 (1) [100%] 1 of 1 ✔[e4/9874dc] process > sv:variantCall:filterCalls (1) [100%] 1 of 1 ✔[d2/79af25] process > sv:variantCall:sortVCF (1) [100%] 1 of 1 ✔[90/c6bd8c] process > sv:annotate_sv_vcf (1) [100%] 1 of 1 ✔[bb/f8f63e] process > sv:runReport:getVersions [100%] 1 of 1, cached: 1 ✔[1c/b14102] process > sv:runReport:getParams [100%] 1 of 1, cached: 1 ✔[51/b15645] process > sv:runReport:report (1) [100%] 1 of 1 ✔[33/820432] process > output_sv (3) [100%] 4 of 4, cached: 1 ✔[90/7d5eb0] process > refine_with_sv (1) [100%] 1 of 1 ✔[fa/a4e1eb] process > concat_refined_snp [100%] 1 of 1 ✔[a4/3c11a4] process > annotate_snp_vcf (1) [100%] 1 of 1 ✔[df/cb5d32] process > concat_snp_vcfs [100%] 1 of 1 ✔[09/148182] process > sift_clinvar_snp_vcf (1) [100%] 1 of 1 ✔[4f/aabbea] process > vcfStats [100%] 1 of 1 ✔[dc/339a31] process > report_snp:getVersions [100%] 1 of 1, cached: 1 ✔[1f/4fdc76] process > report_snp:getParams [100%] 1 of 1, cached: 1 ✔[9c/67e08b] process > report_snp:makeReport (1) [100%] 1 of 1 ✔[28/23509d] process > output_snp (2) [100%] 7 of 7 ✔[4d/a6f1a0] process > cnv_spectre:mosdepth (1) [100%] 1 of 1 ✔[00/ffc48f] process > cnv_spectre:callCNV (1) [100%] 1 of 1 ✔[0b/333333] process > cnv_spectre:bgzip_and_index... [100%] 1 of 1 ✔[cc/168d28] process > cnv_spectre:annotate_vcf (1) [100%] 1 of 1 ✔[ee/e86d4a] process > cnv_spectre:getVersions [100%] 1 of 1 ✔[ac/d7db97] process > cnv_spectre:add_snp_tools_t... [100%] 1 of 1 ✔[37/5f144a] process > cnv_spectre:getParams [100%] 1 of 1 ✔[3d/bb5333] process > cnv_spectre:makeReport (1) [100%] 1 of 1 ✔[53/bd5674] process > output_cnv (1) [100%] 2 of 2 ✔[8f/97acc7] process > str:call_str (1) [100%] 1 of 1 ✔[e6/3d8e0f] process > str:annotate_repeat_expansi... [100%] 1 of 1 ✔[86/a0fcbb] process > str:getVersions [100%] 1 of 1, cached: 1 ✔[cf/0b3aac] process > str:getParams [100%] 1 of 1, cached: 1 ✔[51/e69caf] process > str:bam_region_filter (1) [100%] 1 of 1 ✔[83/17bde7] process > str:bam_read_filter (1) [100%] 1 of 1 ✔[46/d4a751] process > str:generate_str_content (1) [100%] 1 of 1 ✔[0f/ee0054] process > str:concat_str_vcfs [100%] 1 of 1 ✔[c0/2e44be] process > str:merge_tsv [100%] 1 of 1 ✔[e4/b5e958] process > str:make_report (1) [100%] 1 of 1 ✔[56/6aae43] process > output_str (4) [100%] 4 of 4 ✔[9f/35f14a] process > configure_jbrowse (1) [100%] 1 of 1 ✔[94/430e3a] process > combine_metrics_json (1) [100%] 1 of 1 ✔[b2/bef23c] process > publish_artifact (9) [100%] 9 of 9, cached: 7 ✔Completed at: 22-May-2024 17:56:20Duration : 31m 58sCPU hours : 2.8 (3.2% cached)Succeeded : 90Cached : 26
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
No response
The text was updated successfully, but these errors were encountered:
I ran the workflow on the demo dataset provided by this workflow, and I get different results when running --cnv with and without --use_qdnaseq. The reports also look different, with useful graphs present in the version using QDNAseq no longer present with Spectre.
We're working on adding plots to the spectre output, we were keen to get spectre into our users hands as quickly as possible and so visualisations are lagging behind somewhat. Apologies for that.
When running with QDNAseq, I get a CNV for chromosome 20, but I get no CNV when running with Spectre on the same demo dataset.
These are two very different algorithms and so differences are to be expected. It would be great to hear your feedback when you get the two tools running on real samples. Demo data is often not complete as we can't ship huge amounts of data.
Operating System
CentOS 7
DEMO.wf-human-cnv-report_qdnaseq.pdf
DEMO.wf-human-cnv-report_spectre.pdf
Other Linux
No response
Workflow Version
v2.2.0
Workflow Execution
Command line (Cluster)
Other workflow execution
No response
EPI2ME Version
No response
CLI command run
Workflow Execution - CLI Execution Profile
None
What happened?
I ran the workflow on the demo dataset provided by this workflow, and I get different results when running
--cnv
with and without--use_qdnaseq
. The reports also look different, with useful graphs present in the version using QDNAseq no longer present with Spectre.When running with QDNAseq, I get a CNV for chromosome 20, but I get no CNV when running with Spectre on the same demo dataset.
I included the run output for the run with Spectre and the two reports in PDF.
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
No response
The text was updated successfully, but these errors were encountered: