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nf-core / smrnaseq

A small-RNA sequencing analysis pipeline
https://nf-co.re/smrnaseq
MIT License
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MIRDEEP2:MIRDEEP2_RUN failed #221

Closed mianlee closed 9 months ago

mianlee commented 1 year ago

Description of the bug

Dear authors:

The pipeline works fine except for Mirdeep2. It shows MIRDEEP2:MIRDEEP2_RUN failed. I checked all my files and parameters, but I can't solve this issue. Do you what can cause this error? Thank you so much! 屏幕截图 2023-02-02 215516

Command used and terminal output

nextflow run smrnaseq/ --input samplesheet.csv \
--mirna_gtf /home/mli/Desktop/miRNA_Analysis/miRNA_files/hsa.gff3 \
--mature /home/mli/Desktop/miRNA_Analysis/miRNA_files/mature.fa.gz \
--hairpin /home/mli/Desktop/miRNA_Analysis/miRNA_files/hairpin.fa.gz \
--fasta /home/mli/Desktop/miRNA_Analysis/reference/GRCh38.fa \
--bowtie_index /home/mli/Desktop/miRNA_Analysis/reference/GRCh38 \
--mirtrace_species hsa \
--genome GRCh38 \
-profile docker --outdir results

Relevant files

No response

System information

CentOS 7 linux HPC

apeltzer commented 1 year ago

Can you share more information, e.g. logfiles of MIRDEEP2 ?

apeltzer commented 1 year ago

HI @mianlee - we need more details to be able to address this issue. I cannot reproduce at the moment using the testdata. Ideally, please share the details for the failing step, e.g. .command.log and .command.err from the MIRDEEP2 step that fails. I will postpone this for a later release if I dont get a response by then :-)

VojtechBarton commented 1 year ago

Hi, I have run into the similar problem. 3 of my 48 samples failed on MIRDEEP2_RUN with the same message. Going through the logs, and all of them have one thing in common. It all yield "No precursors excised" message in .command.log file.


#####################################
#                                   #
# miRDeep2.0.1.3                   #
#                                   #
# last change: 08/11/2019           #
#                                   #
#####################################

miRDeep2 started at 11:37:14

#Starting miRDeep2
/usr/local/bin/miRDeep2.pl POP6_28d_BAL_B_collapsed.fa genome.edited.fa POP6_28d_BAL_B_reads_vs_refdb.arf mature.fa_igenome.fa_idx.fa none hairpin.fa_igenome.fa_idx.fa -d -z _POP6_28d_BAL_B_collapsed

miRDeep2 started at 11:37:14

mkdir mirdeep_runs/run_23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed

#Starting miRDeep2
#testing input files
started: 11:37:35
sanity_check_mature_ref.pl mature.fa_igenome.fa_idx.fa

#testing input files

ended: 11:37:35
total:0h:0m:0s

sanity_check_reads_ready_file.pl POP6_28d_BAL_B_collapsed.fa

started: 11:37:35

ended: 11:37:35
total:0h:0m:0s

started: 11:37:35
sanity_check_genome.pl genome.edited.fa

ended: 11:37:57
total:0h:0m:22s

started: 11:37:57
sanity_check_mapping_file.pl POP6_28d_BAL_B_reads_vs_refdb.arf

ended: 11:37:57
total:0h:0m:0s

started: 11:37:57
sanity_check_mature_ref.pl hairpin.fa_igenome.fa_idx.fa

ended: 11:37:57
total:0h:0m:0s

started: 11:37:57
Quantitation of expressed miRNAs in data

quantifier.pl -p hairpin.fa_igenome.fa_idx.fa -m mature.fa_igenome.fa_idx.fa  -r POP6_28d_BAL_B_collapsed.fa   -y 23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed -k -d 
#Quantitation of known miRNAs in data
getting samples and corresponding read numbers

Converting input files
building bowtie index
mapping mature sequences against index
mapping read sequences against index
Mapping statistics

#desc   total   mapped  unmapped    %mapped %unmapped
total: 20566    0   20566   0.000   100.000
seq: 20566  0   20566   0.000   100.000
analyzing data
Expressed miRNAs are written to expression_analyses/expression_analyses_23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed/miRNA_expressed.csv
    not expressed miRNAs are written to expression_analyses/expression_analyses_23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed/miRNA_not_expressed.csv

Creating miRBase.mrd file

make_html2.pl -q expression_analyses/expression_analyses_23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed/miRBase.mrd -k mature.fa_igenome.fa_idx.fa -y 23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed -d -o -i expression_analyses/expression_analyses_23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed/mature.fa_igenome.fa_idx.fa_mapped.arf    -M miRNAs_expressed_all_samples_23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed.csv  
miRNAs_expressed_all_samples_23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed.csv file with miRNA expression values
parsing miRBase.mrd file finished

ended: 11:37:59
total:0h:0m:2s

started: 11:37:59
rna2dna.pl mature.fa_igenome.fa_idx.fa > mirdeep_runs/run_23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed/tmp/mature.fa_igenome.fa_idx.fa

rna2dna.pl hairpin.fa_igenome.fa_idx.fa > mirdeep_runs/run_23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed/tmp/hairpin.fa_igenome.fa_idx.fa

ended: 11:37:59
total:0h:0m:0s

#parsing genome mappings
parse_mappings.pl POP6_28d_BAL_B_reads_vs_refdb.arf -a 0 -b 18 -c 25 -i 5 > mirdeep_runs/run_23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed/tmp/POP6_28d_BAL_B_reads_vs_refdb.arf_parsed.arf

started: 11:37:59
#parsing genome mappings

ended: 11:37:59
total:0h:0m:0s

#excising precursors
started: 11:37:59
excise_precursors_iterative_final.pl genome.edited.fa mirdeep_runs/run_23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed/tmp/POP6_28d_BAL_B_reads_vs_refdb.arf_parsed.arf mirdeep_runs/run_23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed/tmp/precursors.fa mirdeep_runs/run_23_06_2023_t_11_37_14_POP6_28d_BAL_B_collapsed/tmp/precursors.coords 50000
#excising precursors
1   0

ended: 11:38:08
total:0h:0m:9s

No precursors excised

**********************************************************************************************************
bounlu commented 1 year ago

I have the same issue that part of my samples fail with miRDeep2 with the same error: No precursors excised

mschilli87 commented 1 year ago

Without a small(!) sharable dataset (and exact miRDeep2 command) that reproduces the error even @Drmirdeep will have a hard time troubleshooting this. Also please note that even though you see the same error message (i.e. 'symptoms'), the underlying cause might be different.

apeltzer commented 1 year ago

I unmilestoned this as this requires further data to support finding a potential cause of the issue. Fully agree with what @mschilli87 said - if you could/can share a small dataset that can be used to track down the issue, please share :)

TOCEAN-ops commented 11 months ago

I had the same problem, No precursors excised This is my code

miRDeep2.pl reads_collapsed.fa Oryza_sativa.fa reads_collapsed_vs_genome.arf osa_mature.fa osa_hairpin.fa none -t osa -g -1 2>report.log

How do you solve it? Thank you very much

mschilli87 commented 11 months ago

@TOCEAN-ops: Did you even read the comments here before commenting yourself? Nothing changed since August: Without being able to reproduce the issue, there won't be a way to help. 🤷

TOCEAN-ops commented 11 months ago

Just wanted to see if it worked out. Wanted to ask

花开再会 @.***

 

------------------ 原始邮件 ------------------ 发件人: "nf-core/smrnaseq" @.>; 发送时间: 2023年12月8日(星期五) 晚上6:06 @.>; @.**@.>; 主题: Re: [nf-core/smrnaseq] MIRDEEP2:MIRDEEP2_RUN failed (Issue #221)

@TOCEAN-ops: Did you even read the comments here before commenting yourself? Nothing changed since August: Without being able to reproduce the issue, there won't be a way to help. 🤷

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apeltzer commented 9 months ago

Should work in dev

Drmirdeep commented 9 months ago

Ok. 0 reads mapped. Why is anyone surprised here that no precursors were excised? The tool cannot be more verbose. But maybe it should directly abort in this case 🤷🏼‍♂️