Error in findColumnWithAllEntries(ids, metadata) : No column contains all vector entries #1445
Description
Description of the bug
Hey, on the current version 3.17.0, I get:
Error in findColumnWithAllEntries(ids, metadata) : No column contains all vector entries
from:
Error executing process > 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (all_samples)'
Command executed [/home/sebastian/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/quantify_pseudo_alignment/../../../modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r]:
This summarizedexperiment.r script seems to look for the geneids in the samplesheet?!
Not sure what goes wrong here.
Version 3.14.0 ran this step successfully just now, and also ran successfully on this fasta/gff before with other read data.
Best
Command used
nextflow run \
nf-core/rnaseq \
-profile singularity \
-resume \
--input samplesheet.csv \
--outdir results_rnaseq \
--gff genome/VCh_C6706_renamed_txfix_agat.gff \
--fasta genome/VCh_C6706_renamed.fa \
--igenomes_ignore \
--genome null \
--skip_biotype_qc \
--skip_rseqc
samplesheet.csv
sample,fastq_1,fastq_2,strandedness,condition,replicate
1A2,reads/1A2_S4_R1_001.fastq.gz,reads/1A2_S4_R2_001.fastq.gz,auto,1,A2
1B2,reads/1B2_S14_R1_001.fastq.gz,reads/1B2_S14_R2_001.fastq.gz,auto,1,B2
1C1,reads/1C1_S24_R1_001.fastq.gz,reads/1C1_S24_R2_001.fastq.gz,auto,1,C1
5A2,reads/5A2_S7_R1_001.fastq.gz,reads/5A2_S7_R2_001.fastq.gz,auto,5,A2
5B2,reads/5B2_S17_R1_001.fastq.gz,reads/5B2_S17_R2_001.fastq.gz,auto,5,B2
5C1,reads/5C1_S27_R1_001.fastq.gz,reads/5C1_S27_R2_001.fastq.gz,auto,5,C1
Output
Command executed [/home/sebastian/.nextflow/assets/nf-core/rnaseq/./workflows/rnaseq/../../subworkflows/nf-core/quantify_pseudo_alignment/../../../modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r]:
Command exit status:
1
Command output:
(empty)
Command error:
3815 VCA1068.1 VCA1068 VCA1068
3816 VCA1069.1 VCA1069 VCA1069
3817 VCA1070.1 VCA1070 VCA1070
3818 VCA1071.1 VCA1071 VCA1071
3819 VCA1072.1 VCA1072 VCA1072
3820 VCA1073.1 VCA1073 VCA1073
3821 VCA1074.1 VCA1074 VCA1074
3822 VCA1075.1 VCA1075 VCA1075
3823 VCA1077.1 VCA1077 VCA1077
3824 VqmR.1 VqmR VqmR
3825 VCA1078.1 VCA1078 VCA1078
3826 VCA1079.1 VCA1079 VCA1079
3827 VCA1080.1 VCA1080 VCA1080
3828 VCA1081.1 VCA1081 VCA1081
3829 VCA1082.1 VCA1082 VCA1082
3830 VCA1084.1 VCA1084 VCA1084
3831 VCA1085.1 VCA1085 VCA1085
3832 VCA1086.1 VCA1086 VCA1086
3833 VCA1087.1 VCA1087 VCA1087
3834 VCA1088.1 VCA1088 VCA1088
3835 VCA1089.1 VCA1089 VCA1089
3836 VCA1090.1 VCA1090 VCA1090
3837 VCA1091.1 VCA1091 VCA1091
3838 VCA1092.1 VCA1092 VCA1092
3839 VCA1093.1 VCA1093 VCA1093
3840 VCA1094.1 VCA1094 VCA1094
3841 VCA1095.1 VCA1095 VCA1095
3842 VCA1096.1 VCA1096 VCA1096
3843 VCA1097.1 VCA1097 VCA1097
3844 VCA1098.1 VCA1098 VCA1098
3845 VCA1099.1 VCA1099 VCA1099
3846 VCA1100.1 VCA1100 VCA1100
3847 VCA1101.1 VCA1101 VCA1101
3848 VCA1102.1 VCA1102 VCA1102
3849 VCA1104.1 VCA1104 VCA1104
3850 VCA1105.1 VCA1105 VCA1105
3851 VCA1106.1 VCA1106 VCA1106
3852 VCA1108.1 VCA1108 VCA1108
3853 VCA1109.1 VCA1109 VCA1109
3854 VCA1110.1 VCA1110 VCA1110
3855 VCA1111.1 VCA1111 VCA1111
3856 VCA1112.1 VCA1112 VCA1112
3857 VCA1113.1 VCA1113 VCA1113
3858 VCA1114.1 VCA1114 VCA1114
3859 VCA1115.1 VCA1115 VCA1115
Error in findColumnWithAllEntries(ids, metadata) :
No column contains all vector entries 16Sa, 16Sb, 16Sc, 16Sd, 16Se, 16Sf, 16Sg, 16Sh, 23Sa, 23Sb, 23Sc, 23Sd, 23Se, 23Sf, 23Sg, 23Sh, 4.5s, 5Sa, 5Sb, 5Sc, 5Sd, 5Se, 5Sf, 5Sg, 5Sh, 6S, aat, aceE, aceF, acpP, acpS, adk, alaS, alr, anmK, ansA, apaG, apaH, araD, argC, argD, argS, aroB, aroE, aroK, artM, artP, asnB, asnC, aspA, aspS, astD, atpC, avtA, b12, bcp, bioD, cadB, carB, cca, ccrB, cdiGMP, clpA, clpP, clpS, clpX, cls, cmk, coaD, coaE, cobS, cobT, cobU, cpdB, cpxA, cpxP, CsrB, CsrC, CsrD, cyaA, cyaY, cysB, cysE, cysM, cysN, cysS, dapA, dapF, dcuC, ddl, def, deoA, deoD, dinG, dipZ, djlA, dnaA, dnaE, dnaG, dnaK, ectC, emrD, engA, engB, eno, envZ, era, fabG, fabZ, fadA, fadB, fadE, fadI, fadJ, fbpC, fieF, fis, FlaX, flgA, flgB, flgC, flgD, flgE, flgF, flgG, flgH, flgI, flgJ, flgK, flgL, flhA, flhB, flhF, fliA, fliD, fliE, fliF, fliG, fliH, fliI, fliJ, fliL, fliM, fliN, fliP, fliQ, fliR, fliS, fmt, folE, fre, frr, frsA, ftsA, ftsB, fumC, fur, fxsA, galM, gcp, GcvB, gidB, glgA,
Calls: parse_metadata -> findColumnWithAllEntries
Execution halted
INFO: Cleaning up image...
Relevant files
No response
System information
Nextflow v24.10.0
64 core desktop server
local executor
singularity
nfcore/rnaseq v3.17.0