Question: Cuffdiff Fatal error: Exit code 1 () Error: number of labels must match number of conditions number of labels must match number of conditions
0
juls.jaeger • 10 wrote:
Hi!
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: | toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.3 |
| Galaxy Tool Version: | 2.2.1.3 |
| 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 |
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modified 3.1 years ago
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Jennifer Hillman Jackson ♦ 25k
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3.1 years ago by
juls.jaeger • 10
