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Differential Expression Analysis Error #46

Closed NanoCoreUSA closed 7 months ago

NanoCoreUSA commented 7 months ago

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v0.4.1

Workflow Execution

EPI2ME Desktop application

EPI2ME Version

v5.1.3

CLI command run

No response

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

I'm attempting to run the 'wf-transcriptomes' workflow within EPI2ME, it completes successfully, but in looking at the overview it seems like the differential expression analysis step didn't complete fully. I've attached the logs below, the relevant error I keep getting is 

Retry deAnalysis with gff format setting.
[ef/4b57ab] NOTE: Process `pipeline:differential_expression:deAnalysis` terminated with an error exit status (1) -- Execution is retried (1)
[8a/9cc039] Re-submitted process > pipeline:differential_expression:deAnalysis

I just want to make sure everything completed successfully before I continue with my analysis (maybe it did?).

Relevant log output

N E X T F L O W  ~  version 23.04.2
Launching `/data/SWINGLE_SPLICING/epi2me/workflows/epi2me-labs/wf-transcriptomes/main.nf` [swingle_splicing] DSL2 - revision: 0c32ada4a1
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-transcriptomes v0.4.1
--------------------------------------------------------------------------------
Core Nextflow options
  runName             : swingle_splicing
  containerEngine     : docker
  launchDir           : /data/SWINGLE_SPLICING/epi2me/instances/wf-transcriptomes_01HFCRRK9NNN3EW0BMQEM14X65
  workDir             : /data/SWINGLE_SPLICING/epi2me/instances/wf-transcriptomes_01HFCRRK9NNN3EW0BMQEM14X65/work
  projectDir          : /data/SWINGLE_SPLICING/epi2me/workflows/epi2me-labs/wf-transcriptomes
  userName            : grid
  profile             : standard
  configFiles         : /data/SWINGLE_SPLICING/epi2me/workflows/epi2me-labs/wf-transcriptomes/nextflow.config
Input Options
  fastq               : /data/SWINGLE_SPLICING/reads
  transcriptome_source: precomputed
  ref_transcriptome   : /home/grid/Insync/GridION/gencode.v44.transcripts.fa.gz
  ref_annotation      : /home/grid/Insync/GridION/gencode.v44.annotation.gff3.gz
Output Options
  out_dir             : /data/SWINGLE_SPLICING/epi2me/instances/wf-transcriptomes_01HFCRRK9NNN3EW0BMQEM14X65/output
Sample Options
  sample_sheet        : /data/SWINGLE_SPLICING/epi2me_sampleSheet.csv
Options for reference-based workflow
  plot_gffcmp_stats   : false
Differential Expression Options
  de_analysis         : true
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-transcriptomes for your analysis please cite:
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-transcriptomes v0.4.1.
--------------------------------------------------------------------------------
Reference Transcriptome provided will be used for differential expression.
Checking fastq input.
[d6/a8dfdf] Submitted process > pipeline:differential_expression:checkSampleSheetCondition
[6f/328124] Submitted process > pipeline:getParams
[50/035d43] Submitted process > validate_sample_sheet
[29/ef5f3d] Submitted process > pipeline:getVersions
[ee/05beeb] Submitted process > pipeline:decompress_transcriptome
[a0/3aef98] Submitted process > pipeline:decompress_annotation
[ea/0dcdb2] Submitted process > pipeline:preprocess_ref_transcriptome
[91/a9aa7b] Submitted process > fastcat (6)
[99/07f375] Submitted process > pipeline:preprocess_ref_annotation
[0e/a55fbd] Submitted process > fastcat (8)
[66/d074c0] Submitted process > pipeline:collectFastqIngressResultsInDir (1)
[fa/ecb585] Submitted process > fastcat (1)
[74/04aa21] Submitted process > pipeline:collectFastqIngressResultsInDir (2)
[f6/9f2f88] Submitted process > fastcat (3)
[a1/1bdc1c] Submitted process > pipeline:collectFastqIngressResultsInDir (3)
[19/e91915] Submitted process > fastcat (7)
[a9/deb741] Submitted process > pipeline:collectFastqIngressResultsInDir (4)
[e6/519589] Submitted process > fastcat (2)
[ce/b3640e] Submitted process > pipeline:collectFastqIngressResultsInDir (5)
[3b/1e1d0b] Submitted process > fastcat (4)
[75/36807f] Submitted process > pipeline:collectFastqIngressResultsInDir (6)
[5a/e8e5f3] Submitted process > fastcat (5)
[8d/fd7349] Submitted process > pipeline:collectFastqIngressResultsInDir (7)
[43/837198] Submitted process > pipeline:differential_expression:build_minimap_index_transcriptome
[b3/146e61] Submitted process > pipeline:preprocess_reads (1)
[24/b76e42] Submitted process > pipeline:preprocess_reads (2)
[21/ecc051] Submitted process > pipeline:preprocess_reads (3)
[90/b16c6a] Submitted process > pipeline:preprocess_reads (4)
[83/8f3e4c] Submitted process > pipeline:preprocess_reads (5)
[e0/9f8ff2] Submitted process > pipeline:preprocess_reads (6)
[ec/a2d025] Submitted process > pipeline:preprocess_reads (7)
[97/9ad351] Submitted process > pipeline:collectFastqIngressResultsInDir (8)
[85/546f17] Submitted process > pipeline:preprocess_reads (8)
[91/c0bb68] Submitted process > pipeline:differential_expression:map_transcriptome (2)
[4a/60281e] Submitted process > pipeline:differential_expression:map_transcriptome (1)
[1b/1005db] Submitted process > pipeline:differential_expression:map_transcriptome (3)
[39/0fb087] Submitted process > pipeline:differential_expression:map_transcriptome (7)
[a1/408f3d] Submitted process > pipeline:differential_expression:map_transcriptome (8)
[3a/1f80db] Submitted process > pipeline:differential_expression:map_transcriptome (6)
[cb/9543a5] Submitted process > pipeline:differential_expression:map_transcriptome (5)
[da/e66728] Submitted process > pipeline:differential_expression:map_transcriptome (4)
[24/06a07c] Submitted process > pipeline:differential_expression:count_transcripts (1)
[58/445428] Submitted process > pipeline:differential_expression:count_transcripts (2)
[04/5214c5] Submitted process > pipeline:differential_expression:count_transcripts (3)
[77/6b7dd9] Submitted process > pipeline:differential_expression:count_transcripts (4)
[8d/524e63] Submitted process > pipeline:differential_expression:count_transcripts (5)
[b4/c23c54] Submitted process > pipeline:differential_expression:count_transcripts (6)
[01/7f2741] Submitted process > pipeline:differential_expression:count_transcripts (7)
[cf/e23f4b] Submitted process > pipeline:differential_expression:count_transcripts (8)
[54/972128] Submitted process > pipeline:differential_expression:mergeCounts
[c6/c75daa] Submitted process > pipeline:differential_expression:mergeTPM
[ef/4b57ab] Submitted process > pipeline:differential_expression:deAnalysis
Retry deAnalysis with gff format setting.
[ef/4b57ab] NOTE: Process `pipeline:differential_expression:deAnalysis` terminated with an error exit status (1) -- Execution is retried (1)
[8a/9cc039] Re-submitted process > pipeline:differential_expression:deAnalysis
[fb/62a550] Submitted process > pipeline:differential_expression:plotResults
[91/554478] Submitted process > pipeline:makeReport (1)
[0b/cbd2e8] Submitted process > output (16)
[7c/de7c79] Submitted process > output (10)
[7e/f55238] Submitted process > output (15)
[a2/81c7c0] Submitted process > output (7)
[0a/6fa1f6] Submitted process > output (4)
[e2/52b5c3] Submitted process > output (9)
[9f/bb18cf] Submitted process > output (2)
[32/d6472c] Submitted process > output (3)
[44/2c2533] Submitted process > output (13)
[38/6dc357] Submitted process > output (12)
[af/0e0960] Submitted process > output (14)
[d6/50a2dd] Submitted process > output (5)
[c2/cf1c35] Submitted process > output (6)
[31/eaf231] Submitted process > output (1)
[cd/7ada53] Submitted process > output (8)
[df/35b69d] Submitted process > output (11)
[de/d59f55] Submitted process > output (24)
[7f/31ccd8] Submitted process > output (19)
[27/59ab84] Submitted process > output (23)
[20/c16d8d] Submitted process > output (21)
[19/f3acbb] Submitted process > output (18)
[e5/361d38] Submitted process > output (17)
[57/e93f9d] Submitted process > output (20)
[51/da3d5e] Submitted process > output (22)
Waiting for file transfers to complete (1 files)

Application activity log entry

No response

sarahjeeeze commented 7 months ago

Hi, that error message is expected. The workflow will just retry that step with settings for gtf and then gff to overcome an issue where some users input a file with a '.gtf' extension that seem to actually be in '.gff3' format. Both are accepted.

NanoCoreUSA commented 7 months ago

Ah gotcha, thanks for the explanation!