Open OliverH96 opened 3 months ago
Tried again on latest version (2.3.1) and getting the same error.
Hi @OliverH96,
for now you could try to pass the additional argument --database
to mirtop using a custom config. This would require adding something like:
process {
withName: 'MIRTOP_QUANT' {
ext.args = "--database RumimiR"
}
}
You have to check if RumimiR
is the term used in your provided gff. As far as I understand, mirtop
searches for known tags in the gff file and therefore fails in your case.
Hi @OliverH96, for now you could try to pass the additional argument
--database
to mirtop using a custom config. This would require adding something like:process { withName: 'MIRTOP_QUANT' { ext.args = "--database RumimiR" } }
You have to check if
RumimiR
is the term used in your provided gff. As far as I understand,mirtop
searches for known tags in the gff file and therefore fails in your case.
Apologies for getting back to you so late. This did seem to advance the pipeline slightly, but am now getting a different error:
ERROR ~ Error executing process > 'NFCORE_SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT'
Caused by:
Process `NFCORE_SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT` terminated with an error exit status (1)
Command executed:
#Cleanup the GTF if mirbase html form is broken
GTF="rumimir_sheep.gff"
sed 's/>/>/g' $GTF | sed 's#<br>#\n#g' | sed 's#</p>##g' | sed 's#<p>##g' | sed -e :a -e '/^\n*$/{$d;N;};/\n$/ba' > ${GTF}_html_cleaned.gtf
mirtop gff --hairpin hairpin.fa_igenome.fa_idx.fa --gtf ${GTF}_html_cleaned.gtf -o mirtop --sps oar ./bams/*
mirtop counts --hairpin hairpin.fa_igenome.fa_idx.fa --gtf ${GTF}_html_cleaned.gtf -o mirtop --sps oar --add-extra --gff mirtop/mirtop.gff
mirtop export --format isomir --hairpin hairpin.fa_igenome.fa_idx.fa --gtf ${GTF}_html_cleaned.gtf --sps oar -o mirtop mirtop/mirtop.gff
mirtop stats mirtop/mirtop.gff --out mirtop/stats
mv mirtop/stats/mirtop_stats.log mirtop/stats/full_mirtop_stats.log
cat <<-END_VERSIONS > versions.yml
"NFCORE_SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT":
mirtop: $(echo $(mirtop --version 2>&1) | sed 's/^.*mirtop //')
END_VERSIONS
Command exit status:
1
Command output:
['gff', '--hairpin', 'hairpin.fa_igenome.fa_idx.fa', '--gtf', 'rumimir_sheep.gff_html_cleaned.gtf', '-o', 'mirtop', '--sps', 'oar', './bams/Sire_A_8324_Control_seqcluster.bam', './bams/Sire_A_8401_Control_seqcluster.bam', './bams/Sire_A_8631_Biosolids_seqcluster.bam', './bams/Sire_A_8698_Biosolids_seqcluster.bam', './bams/Sire_B_8335_Control_seqcluster.bam', './bams/Sire_B_8433_Control_seqcluster.bam', './bams/Sire_B_8607_Biosolids_seqcluster.bam', './bams/Sire_B_8796_Biosolids_seqcluster.bam', './bams/Sire_C_8235_Control_seqcluster.bam', './bams/Sire_C_8431_Control_seqcluster.bam', './bams/Sire_C_8747_Biosolids_seqcluster.bam', './bams/Sire_C_8767_Biosolids_seqcluster.bam', './bams/Sire_D_8231_Control_seqcluster.bam', './bams/Sire_D_8416_Control_seqcluster.bam', './bams/Sire_D_8744_Biosolids_seqcluster.bam', './bams/Sire_D_8758_Biosolids_seqcluster.bam']
Command error:
/usr/local/lib/python3.9/site-packages/mirtop/mirna/mintplates.py:512: SyntaxWarning: "is" with a literal. Did you mean "=="?
if prefix is '':
05/02/2024 05:12:45 INFO Run annotation
05/02/2024 05:12:45 INFO Database different than miRBase or MirGeneDB
05/02/2024 05:12:45 INFO If you get an error when loading,
05/02/2024 05:12:45 INFO report it to https://github.com/miRTop/mirtop/issues
['gff', '--hairpin', 'hairpin.fa_igenome.fa_idx.fa', '--gtf', 'rumimir_sheep.gff_html_cleaned.gtf', '-o', 'mirtop', '--sps', 'oar', './bams/Sire_A_8324_Control_seqcluster.bam', './bams/Sire_A_8401_Control_seqcluster.bam', './bams/Sire_A_8631_Biosolids_seqcluster.bam', './bams/Sire_A_8698_Biosolids_seqcluster.bam', './bams/Sire_B_8335_Control_seqcluster.bam', './bams/Sire_B_8433_Control_seqcluster.bam', './bams/Sire_B_8607_Biosolids_seqcluster.bam', './bams/Sire_B_8796_Biosolids_seqcluster.bam', './bams/Sire_C_8235_Control_seqcluster.bam', './bams/Sire_C_8431_Control_seqcluster.bam', './bams/Sire_C_8747_Biosolids_seqcluster.bam', './bams/Sire_C_8767_Biosolids_seqcluster.bam', './bams/Sire_D_8231_Control_seqcluster.bam', './bams/Sire_D_8416_Control_seqcluster.bam', './bams/Sire_D_8744_Biosolids_seqcluster.bam', './bams/Sire_D_8758_Biosolids_seqcluster.bam']
Traceback (most recent call last):
File "/usr/local/bin/mirtop", line 10, in <module>
sys.exit(main())
File "/usr/local/lib/python3.9/site-packages/mirtop/command_line.py", line 31, in main
reader(kwargs["args"])
File "/usr/local/lib/python3.9/site-packages/mirtop/gff/__init__.py", line 28, in reader
matures = mapper.read_gtf_to_precursor(args.gtf)
File "/usr/local/lib/python3.9/site-packages/mirtop/mirna/mapper.py", line 172, in read_gtf_to_precursor
mapped = read_gtf_to_precursor_mirbase(gtf)
File "/usr/local/lib/python3.9/site-packages/mirtop/mirna/mapper.py", line 333, in read_gtf_to_precursor_mirbase
id_dict[idname[0]] = name[0]
IndexError: list index out of range
Work dir:
/gpfs01/home/sbzoh/F1_Seminal_Plasma_RNA/work/bb/f388eaca99ec7268114f74a3fb2490
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '.nextflow.log' file for details
Description of the bug
I'm using sheep miRNA data. miRBase contains a few entries for sheep miRNAs but does not provide a gff file on it's download page. I instead used a gff of sheep miRNAs from the RumimiR database (https://rumimir.sigenae.org/), but reach an error at the mirtop_quant step.
I've uploaded the gff file used, but appended the file extension to .txt to allow for uploading.
My params file: input: '/gpfs01/home/sbzoh/F1_Seminal_Plasma_RNA/rawData/Fastq/F1_SeminalPlasma_Samplesheet.csv' outdir: '/gpfs01/home/sbzoh/F1_Seminal_Plasma_RNA/smrnaseq_output' with_umi: false mirtrace_species: 'oar' fasta: '/gpfs01/home/sbzoh//refGenome/Ovis_aries_rambouillet.ARS-UI_Ramb_v2.0.dna.toplevel.fasta' mirna_gtf: '/gpfs01/home/sbzoh//refGenome/rumimir_sheep.gff' mature: '/gpfs01/home/sbzoh//refGenome/mature.fa' hairpin: '/gpfs01/home/sbzoh//refGenome/hairpin.fa' filter_contamination: false skip_mirdeep: true
Command used and terminal output
Relevant files
nextflow.log rumimir_sheep.txt
System information
Nextflow version (23.10.1) Hardware (HPC) Executor (slurm) Container engine: (Singularity) OS (CentOS Linux) Version of nf-core/smrnaseq (2.3.0)