Question: miRDeep2 "no file 'precursors.fa_stack' found" error.
0
gravatar for YJ
11 months ago by
YJ0
YJ0 wrote:

Hello everyone!

I was trying to run miRDeep2 for a project on novel miRNA discovery from transcriptomic data, however, this error pops up when I try to run the "mirdeep2.pl" script with appropriate parameters.

The error:

#excising precursors
#excising precursors
started: 15:50:33
excise_precursors_iterative_final.pl /home/lab7/Project/newgenome.fa mirdeep_runs/run_28_08_2019_t_15_49_37/tmp/reads_vs_refdb.arf_parsed.arf mirdeep_runs/run_28_08_2019_t_15_49_37/tmp/precursors.fa mirdeep_runs/run_28_08_2019_t_15_49_37/tmp/precursors.coords -1
No file mirdeep_runs/run_28_08_2019_t_15_49_37/tmp/precursors.fa_stack found

Am I messing something up with my parameters? My command is as follows:

date && time miRDeep2.pl ~/Project/reads_collapsed.fa ~/Project/newgenome.fa ~/Project/reads_vs_refdb.arf ~/Project/new_human_mature.fasta none ~/Project/new_human_stem.fasta -t Human -g -1 hsa -v

Note: The " -g -1 " parameter was added after I tried running the script without it, because I saw it on an online forum. Either way, the script with default "-g" parameter or "-g -1" fails to run.

Also, here is the entire dialogue on the terminal from start to end:

(Syntax: newgenome.fa - reference genome file

reads_collapsed.fa - deep sequencing reads collapsed by mapper.pl

reads_vs_refdb.arf - mapped file created by mapper.pl

new_human_mature.fasta - FASTA file containing mature miRNAs from mirBase

new_human_stem.fasta - FASTA file containing precursor/stem sequences from mirBase)

date && time miRDeep2.pl ~/Project/reads_collapsed.fa ~/Project/newgenome.fa ~/Project/reads_vs_refdb.arf ~/Project/new_human_mature.fasta none ~/Project/new_human_stem.fasta -t Human -g -1 hsa -v
Wed Aug 28 15:49:37 EST 2019


    #####################################
    #                                   #
    # miRDeep2.0.1.2                    #
    #                                   #
    # last change: 22/01/2019           #
    #                                   #
    #####################################

    miRDeep2 started at 15:49:37


    #Starting miRDeep2
    #Starting miRDeep2
    /home/lab7/Project/Softwares/mirdeep2-master/bin/miRDeep2.pl /home/lab7/Project/reads_collapsed.fa /home/lab7/Project/newgenome.fa /home/lab7/Project/reads_vs_refdb.arf /home/lab7/Project/new_human_mature.fasta none /home/lab7/Project/new_human_stem.fasta -t Human -g -1 hsa -v

    miRDeep2 started at 15:49:37


    mkdir mirdeep_runs/run_28_08_2019_t_15_49_37

    Use of uninitialized value $tmps in split at /home/lab7/Project/Softwares/mirdeep2-master/bin/miRDeep2.pl line 350, <IN> line 1.
    Use of uninitialized value in pattern match (m//) at /home/lab7/Project/Softwares/mirdeep2-master/bin/miRDeep2.pl line 354, <IN> line 1.
    Use of uninitialized value $tmps in split at /home/lab7/Project/Softwares/mirdeep2-master/bin/miRDeep2.pl line 377.
    #testing input files
    #testing input files
    started: 15:50:33
    sanity_check_mature_ref.pl /home/lab7/Project/new_human_mature.fasta


    ended: 15:50:33
    total:0h:0m:0s

    sanity_check_reads_ready_file.pl /home/lab7/Project/reads_collapsed.fa

    started: 15:50:33

    ended: 15:50:33
    total:0h:0m:0s

    started: 15:50:33
    sanity_check_genome.pl /home/lab7/Project/newgenome.fa


    ended: 15:50:33
    total:0h:0m:0s

    started: 15:50:33
    sanity_check_mapping_file.pl /home/lab7/Project/reads_vs_refdb.arf


    ended: 15:50:33
    total:0h:0m:0s

    started: 15:50:33
    sanity_check_mature_ref.pl /home/lab7/Project/new_human_stem.fasta


    ended: 15:50:33
    total:0h:0m:0s

    started: 15:50:33
    Quantitation of expressed miRNAs in data


    #Quantitation of known miRNAs in data
    quantifier.pl -p /home/lab7/Project/new_human_stem.fasta -m /home/lab7/Project/new_human_mature.fasta  -r /home/lab7/Project/reads_collapsed.fa  -t Human -y 28_08_2019_t_15_49_37 -k  

    ended: 15:50:33
    total:0h:0m:0s

    started: 15:50:33
    rna2dna.pl /home/lab7/Project/new_human_mature.fasta > mirdeep_runs/run_28_08_2019_t_15_49_37/tmp/new_human_mature.fasta

    rna2dna.pl /home/lab7/Project/new_human_stem.fasta > mirdeep_runs/run_28_08_2019_t_15_49_37/tmp/new_human_stem.fasta


    ended: 15:50:33
    total:0h:0m:0s

    #parsing genome mappings
    #parsing genome mappings
    parse_mappings.pl /home/lab7/Project/reads_vs_refdb.arf -a 0 -b 18 -c 25 -i 5 > mirdeep_runs/run_28_08_2019_t_15_49_37/tmp/reads_vs_refdb.arf_parsed.arf

    started: 15:50:33

    ended: 15:50:33
    total:0h:0m:0s

    #excising precursors
    #excising precursors
    started: 15:50:33
    excise_precursors_iterative_final.pl /home/lab7/Project/newgenome.fa mirdeep_runs/run_28_08_2019_t_15_49_37/tmp/reads_vs_refdb.arf_parsed.arf mirdeep_runs/run_28_08_2019_t_15_49_37/tmp/precursors.fa mirdeep_runs/run_28_08_2019_t_15_49_37/tmp/precursors.coords -1
    No file mirdeep_runs/run_28_08_2019_t_15_49_37/tmp/precursors.fa_stack found

    real    0m57.660s
    user    0m13.274s
    sys 0m3.129s
mirna mirdeep2 rna-seq • 524 views
ADD COMMENTlink modified 11 months ago by Ziliang Luo0 • written 11 months ago by YJ0
0
gravatar for Rituriya
11 months ago by
Rituriya30
Canada
Rituriya30 wrote:

Re-run by replacing the last portion of your command: '-t Human -g -1 hsa -v' with '-t hsa'.

ADD COMMENTlink written 11 months ago by Rituriya30

Did that. Still the same error. Is there any other workaround for this?

ADD REPLYlink written 11 months ago by YJ0
0
gravatar for Ziliang Luo
11 months ago by
Ziliang Luo0 wrote:

before "precursors.fa_stack found" error came out and killed the program. it reported excision of precursor at certain iteration. e.g

#excising precursors
...
46  217072
47  210636
48  204216
49  198362
No file mirdeep_runs/run_28_08_2019_t_15_49_37/tmp/precursors.fa_stack found

What I did is set the -g option just bigger than where it stopped. For example, -g 200000. Then it can continue the precursor excision. I also tried -g -1 which worked as well. I guess it's because something wrong with the number of the precursor excision.

ADD COMMENTlink written 11 months ago by Ziliang Luo0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 711 users visited in the last hour