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