nf-core / nf-core/genomeannotator
rnaseq_align.nf error
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Nobody has claimed this yet.
bug
- Dominant language
- Nextflow
- Stars
- 44
- Forks
- 17
- PR merge metrics
- No merged PRs in 30d
Description
Description of the bug
Hi! I'm using genomeannotator for the assembly annotation of a microalgae. As inputs I have the assembly, some RNA-Seq libraries and a protein database created by myself.
Command used and terminal output
nextflow run nf-core/genomeannotator -r cbd878f -profile docker --assembly ../Assembly/Canu/Pilon_results/pilon_pilon_3/pilon_pilon_3.fasta --proteins uniref90.fasta --rnaseq_samples ../RNASeq_fastq/rnaseq_samples.csv --max_intron_size 5000 --outdir . --aug_species toxoplasma --spaln_taxon toxogond --aug_config_dir . --aug_config_container . -c config_genomeannotator.txt
Nextflow 23.10.1 is available - Please consider updating your version to it
N E X T F L O W ~ version 23.10.0
Launching `https://github.com/nf-core/genomeannotator` [jovial_brenner] DSL2 - revision: cbd878f7997d367ccbe952648e114ad25962963f
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nf-core/genomeannotator v1.0dev
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Core Nextflow options
runName : jovial_brenner
containerEngine : docker
launchDir : /media/Assembly_annotation
workDir : /media/Assembly_annotation/work
projectDir : /home/fperez/.nextflow/assets/nf-core/genomeannotator
userName : fperez
profile : docker
configFiles : /home/fperez/.nextflow/assets/nf-core/genomeannotator/nextflow.config, /media/Assembly_annotation/config_genomeannotator.txt
Input/output options
assembly : ../Assembly/Canu/Pilon_results/pilon_pilon_3/pilon_pilon_3.fasta
outdir : .
rnaseq_samples : ../RNASeq_fastq/rnaseq_samples.csv
proteins : uniref90.fasta
Options for pipeline behavior
max_intron_size : 5000
dummy_gff : /home/fperez/.nextflow/assets/nf-core/genomeannotator/assets/empty.gff3
Options for ab-initio gene finding
aug_species : toxoplasma
aug_config_container: .
aug_config_dir : .
Options for protein data processing
spaln_taxon : toxogond
Options for PASA behavior
pasa_config_file : /home/fperez/.nextflow/assets/nf-core/genomeannotator/assets/pasa/alignAssembly.config
Options for EvidenceModeler behavior
evm_weights : /home/fperez/.nextflow/assets/nf-core/genomeannotator/assets/evm/weights.txt
!! Only displaying parameters that differ from the pipeline defaults !!
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If you use nf-core/genomeannotator for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/genomeannotator/blob/master/CITATIONS.md
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executor > local (3)
[0b/7e3452] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:AUGUSTUS_STAGECONFIG (Assembly_annotation) [ 0%] 0 of 1
executor > local (4)
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:AUGUSTUS_STAGECONFIG (Assembly_annotation) -
[52/f5d136] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:ASSEMBLY_PREPROCESS:GAAS_ASSEMBLYFILTERBYSIZE (pilon_pilon_3) [100%] 1 of 1, cached: 1 ✔
[3d/6cb819] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:ASSEMBLY_PREPROCESS:GAAS_FASTACLEANER (pilon_pilon_3) [100%] 1 of 1, cached: 1 ✔
[6e/2e3768] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:ASSEMBLY_PREPROCESS:GAAS_FASTASTATISTICS (pilon_pilon_3) [100%] 1 of 1, cached: 1 ✔
[8f/5e4436] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:REPEATMODELER (pilon_pilon_3) [ 0%] 0 of 1
[69/78da24] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:REPEATMASKER:FASTASPLITTER (pilon_pilon_3 - pilon_pilon_3.filtered.clean.fa) [100%] 1 of 1, cached: 1 ✔
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:REPEATMASKER:GUNZIP -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:REPEATMASKER:REPEATMASKER_STAGELIB -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:REPEATMASKER:REPEATMASKER_REPEATMASK -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:REPEATMASKER:REPEATMASKER_CAT_FASTA -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:SPALN_ALIGN_PROTEIN:GAAS_FASTACLEANER (uniref90) -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:SPALN_ALIGN_PROTEIN:EXONERATE_FASTACLEAN -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:SPALN_ALIGN_PROTEIN:GAAS_FASTAFILTERBYSIZE -
[00/d29213] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:SPALN_ALIGN_PROTEIN:SPALN_MAKEINDEX (pilon_pilon_3) [100%] 1 of 1, cached: 1 ✔
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:SPALN_ALIGN_PROTEIN:SPALN_ALIGN -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:SPALN_ALIGN_PROTEIN:SPALN_MERGE -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:SPALN_ALIGN_PROTEIN:AUGUSTUS_ALIGNTOHINTS -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:SPALN_ALIGN_PROTEIN:HELPER_SPALNTOGMOD -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:SPALN_ALIGN_PROTEIN:HELPER_SPALNTOEVM -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:SPALN_ALIGN_PROTEIN:HELPER_SPALNTOTRAINING -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:RNASEQ_ALIGN:STAR_INDEX (pilon_pilon_3) -
[bd/e4c8f6] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:RNASEQ_ALIGN:SAMPLESHEET_CHECK (rnaseq_samples.csv) [100%] 1 of 1, cached: 1 ✔
[eb/fb6e74] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:RNASEQ_ALIGN:FASTP (All) [100%] 1 of 1, cached: 1 ✔
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:RNASEQ_ALIGN:CAT_FASTQ -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:RNASEQ_ALIGN:STAR_ALIGN_PASS_ONE -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:RNASEQ_ALIGN:STAR_ALIGN_PASS_TWO -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:SAMTOOLS_MERGE -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:AUGUSTUS_BAM2HINTS -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:AUGUSTUS_PIPELINE:FASTASPLITTER -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:AUGUSTUS_PIPELINE:AUGUSTUS_AUGUSTUSBATCH -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:AUGUSTUS_PIPELINE:AUGUSTUS_FIXJOINGENES -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:AUGUSTUS_PIPELINE:AUGUSTUS_CREATEGFFIDS -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:AUGUSTUS_PIPELINE:AUGUSTUS_GFF2PROTEINS -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:MULTIQC -
ERROR ~ fromIndex = -1
-- Check script '/home/fperez/.nextflow/assets/nf-core/genomeannotator/./workflows/../subworkflows/local/rnaseq_align.nf' at line: 35 or see '.nextflow.log' file for more details
Relevant files
The custom config file looks like this:
docker {
enabled = true
temp = "/Genome/Assembly_annotation/tmp"
}
env {
TMPDIR = "/Genome/Assembly_annotation/tmp"
TMP = "/Genome/Assembly_annotation/tmp"
}
System information
No response
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with workflows/../subworkflows/local/rnaseq_align.nf at line 35 and inspect .nextflow.log alongside the reported command. Review the custom Docker and temporary-directory configuration, then reproduce the failure and confirm that the RNA-seq alignment stage completes without the fromIndex error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker
- Domain
- data-engineering
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100