Question: Cuffdiff Fatal error: Exit code 1 () Error: number of labels must match number of conditions number of labels must match number of conditions
gravatar for juls.jaeger
3.1 years ago by
United Kingdom
juls.jaeger10 wrote:


I ran into a problem using Cuffdiff. (I am using a local version of galaxy).

When I try to run cuffdiff with my bam files I get the error message:


"An error occurred with this dataset:Fatal error: Exit code 1 () Error: number of labels must match number" for every dataset

Here is the detailed cuffdiff job: does anyone have an idea what the problem could be?

Many thanks in advance, Julian

Tool: Cuffdiff
Name: Cuffdiff on data 79, data 110, and others: transcript FPKM tracking
Created: Fri Oct 23 09:55:17 2015 (UTC)
Filesize: 0 bytes
Dbkey: ?
Format: tabular
Galaxy Tool ID:
Galaxy Tool Version:
Tool Version: cuffdiff v2.2.1 (4237)
Tool Standard Output: stdout
Tool Standard Error: stderr
Tool Exit Code: 1
API ID: f74d8deee55f4712
History ID: 0a248a1f62a0cc04
UUID: 88d22840-bc9c-4469-bb9b-6bd2eb31ddb6
Full Path: /home/julian/galaxy/database/files/000/dataset_800.dat
Job Command-Line: cuffdiff --no-update-check --FDR=0.05 --num-threads="${GALAXY_SLOTS:-4}" --min-alignment-count=10 --library-norm-method=geometric --dispersion-method=pooled -u -b /media/julian/myDATA/RNAseqDATA/gencode FASTA/GRCm38.p4.genome.fa --labels 'wt','het' /media/julian/myDATA/RNAseqDATA/GTFs/gencode.vM7.all_chr_patch_hapl_scaff.annotation.gff3 /media/julian/myDATA/RNAseqDATA/20151022_REX_dedub_bam_files/SC648670_WT_accepted_hits.dedup.bam,/media/julian/myDATA/RNAseqDATA/20151022_REX_dedub_bam_files/SC648913_WT_accepted_hits.dedup.bam,/media/julian/myDATA/RNAseqDATA/20151022_REX_dedub_bam_files/SC648914_WT_accepted_hits.dedup.bam,/media/julian/myDATA/RNAseqDATA/20151022_REX_dedub_bam_files/SC648915_WT_accepted_hits.dedup.bam,/media/julian/myDATA/RNAseqDATA/20151022_REX_dedub_bam_files/SC648917_WT_accepted_hits.dedup.bam /media/julian/myDATA/RNAseqDATA/20151022_REX_dedub_bam_files/SC648671_HET_accepted_hits.dedup.bam,/media/julian/myDATA/RNAseqDATA/20151022_REX_dedub_bam_files/SC648916_HET_accepted_hits.dedup.bam,/media/julian/myDATA/RNAseqDATA/20151022_REX_dedub_bam_files/SC648918_HET_accepted_hits.dedup.bam,/media/julian/myDATA/RNAseqDATA/20151022_REX_dedub_bam_files/SC648920_HET_accepted_hits.dedup.bam,/media/julian/myDATA/RNAseqDATA/20151022_REX_dedub_bam_files/SC648921_HET_accepted_hits.dedup.bam
Job End Time 2015-10-23 10:55:22
Job Start Time 2015-10-23 10:55:20
Cores Allocated 1
Job Runtime (Wall Clock) 2 seconds


Input Parameter Value Note for rerun
Transcripts 78: gencode.vM7.all_chr_patch_hapl_scaff.annotation.gff3  
Omit Tabular Datasets False  
Generate SQLite False  
Input data type BAM  
Name wt  
Replicates 101: SC648670_WT_accepted_hits.dedup.bam, 103: SC648913_WT_accepted_hits.dedup.bam, 104: SC648914_WT_accepted_hits.dedup.bam, 105: SC648915_WT_accepted_hits.dedup.bam, 107: SC648917_WT_accepted_hits.dedup.bam  
Name het  
Replicates 102: SC648671_HET_accepted_hits.dedup.bam, 106: SC648916_HET_accepted_hits.dedup.bam, 108: SC648918_HET_accepted_hits.dedup.bam, 109: SC648920_HET_accepted_hits.dedup.bam, 110: SC648921_HET_accepted_hits.dedup.bam  
Library normalization method geometric  
Dispersion estimation method pooled  
False Discovery Rate 0.05  
Min Alignment Count 10  
Use multi-read correct True  
Perform Bias Correction Yes  
Reference sequence data history  
Using reference file 79: GRCm38.p4.genome.fa  
Include Read Group Datasets No  
Include Count Based output files No  
apply length correction cufflinks effective length correction  
Set Additional Parameters for single end reads? (not recommended for paired-end reads) No  
Set Advanced Cuffdiff parameters? No
ADD COMMENTlink modified 3.1 years ago by Jennifer Hillman Jackson25k • written 3.1 years ago by juls.jaeger10
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This error can come up when the condition names contain spaces or odd characters (alphanumeric and underscores are known to be accepted). I see that the "info" form and command-line have capture single-word condition names, but these could be parsed versions of what was actually entered into the tool form. Use the "re-run" button for one of the error datasets to examine the tool form to review the names entered at run-time and adjust as needed.

If this turns out to not be the root cause of the problem, let us know and we can try other troubleshooting. Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson25k
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