Hi all,
i am using the script miRDeep2.pl, i use this command line :
At first, the program is running correctly, but when i came to the randfold p-values step i obtain this :
Followed by other errors in the next scripts, i think my input files are ok.
Anyone have an idea ? i am lost
i am using the script miRDeep2.pl, i use this command line :
Code:
miRDeep2.pl reads.fa genome.fa reads_vs_genome.arf none none none
#computing randfold p-values
#computing randfold p-values
select_for_randfold.pl mirdeep_runs/run_27_03_2012_t_18_14_41/tmp/signature.arf mirdeep_runs/run_27_03_2012_t_18_14_41/tmp/precursors.str > mirdeep_runs/run_27_03_2012_t_18_14_41/tmp/precursors_for_randfold.ids
started: 18:15:23
Use of uninitialized value $id in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 617.
Use of uninitialized value $id in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 618.
Use of uninitialized value $id in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 619.
Use of uninitialized value $id in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 620.
Use of uninitialized value $db_old in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 260.
Use of uninitialized value $struct in length at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 261.
Use of uninitialized value $db_old in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 289.
Use of uninitialized value $db_old in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 290.
Use of uninitialized value $db_old in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 291.
Use of uninitialized value $seq in length at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 292.
Use of uninitialized value $query in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 424.
Use of uninitialized value $query in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 425.
Use of uninitialized value $query in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 437.
Use of uninitialized value $end in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 682.
Use of uninitialized value $beg in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 682.
Use of uninitialized value $seq in length at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 686.
Use of uninitialized value $beg in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 686.
Use of uninitialized value $beg in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $beg in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $end in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $seq in substr at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $strand in string eq at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 692.
Use of uninitialized value $struct in length at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 707.
Use of uninitialized value $end in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 710.
Use of uninitialized value $beg in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 710.
Use of uninitialized value $struct in length at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 714.
Use of uninitialized value $beg in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 714.
Use of uninitialized value $beg in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 717.
Use of uninitialized value $beg in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 717.
Use of uninitialized value $end in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 717.
Use of uninitialized value $struct in substr at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 717.
Use of uninitialized value $strand in string eq at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 450.
Use of uninitialized value $end in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 682.
Use of uninitialized value $beg in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 682.
Use of uninitialized value $seq in length at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 686.
Use of uninitialized value $beg in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 686.
Use of uninitialized value $beg in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $beg in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $end in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $seq in substr at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $strand in string eq at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 692.
#computing randfold p-values
select_for_randfold.pl mirdeep_runs/run_27_03_2012_t_18_14_41/tmp/signature.arf mirdeep_runs/run_27_03_2012_t_18_14_41/tmp/precursors.str > mirdeep_runs/run_27_03_2012_t_18_14_41/tmp/precursors_for_randfold.ids
started: 18:15:23
Use of uninitialized value $id in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 617.
Use of uninitialized value $id in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 618.
Use of uninitialized value $id in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 619.
Use of uninitialized value $id in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 620.
Use of uninitialized value $db_old in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 260.
Use of uninitialized value $struct in length at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 261.
Use of uninitialized value $db_old in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 289.
Use of uninitialized value $db_old in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 290.
Use of uninitialized value $db_old in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 291.
Use of uninitialized value $seq in length at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 292.
Use of uninitialized value $query in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 424.
Use of uninitialized value $query in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 425.
Use of uninitialized value $query in hash element at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 437.
Use of uninitialized value $end in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 682.
Use of uninitialized value $beg in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 682.
Use of uninitialized value $seq in length at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 686.
Use of uninitialized value $beg in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 686.
Use of uninitialized value $beg in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $beg in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $end in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $seq in substr at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $strand in string eq at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 692.
Use of uninitialized value $struct in length at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 707.
Use of uninitialized value $end in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 710.
Use of uninitialized value $beg in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 710.
Use of uninitialized value $struct in length at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 714.
Use of uninitialized value $beg in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 714.
Use of uninitialized value $beg in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 717.
Use of uninitialized value $beg in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 717.
Use of uninitialized value $end in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 717.
Use of uninitialized value $struct in substr at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 717.
Use of uninitialized value $strand in string eq at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 450.
Use of uninitialized value $end in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 682.
Use of uninitialized value $beg in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 682.
Use of uninitialized value $seq in length at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 686.
Use of uninitialized value $beg in numeric le (<=) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 686.
Use of uninitialized value $beg in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $beg in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $end in subtraction (-) at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $seq in substr at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 689.
Use of uninitialized value $strand in string eq at /home/me/Desktop/mirdeep2/select_for_randfold.pl line 692.
Anyone have an idea ? i am lost

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