#16 Syn-nonsyn-at-position.pl error: Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 31.

[Anonymous]

Originally created by: maxlong... (code.google.com)@gmail.com

What steps will reproduce the problem?
1. calling Syn-nonsyn-at-position.pl
2. Syn-nonsyn-at-position.pl --measure pi --gtf scaffolds.gtf --pileup MciFI_Lar_1_vs_MciFI_Lar_2.filtsorted.pairs.sorted.pileup --codon-table /data/programs/popoolation_1.2.2/syn-nonsyn/codon-table.txt --nonsyn-length-table /data/programs/popoolation_1.2.2/syn-nonsyn/nsl_p1.txt --output MciFI_SSNS.file --snp-output MciFI_SSNS.snp.file --pool-size 24 --min-count 2 --min-coverage 4

3. Here is a view of my gtf file

bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni    ALN     gene    4222    10096   1746    +       .    gene_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; transcript_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"
bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni    ALN     start_codon     4222    4224    202     +    0gene_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; transcript_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni";
bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni    ALN     cds     4222    4303    202     +       0    gene_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; transcript_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; exon_number 1; 1 28 +
bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni    ALN     cds     6111    6223    234     +       2    gene_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; transcript_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; exon_number 2; 29 66 +
bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni    ALN     cds     6479    6706    426     +       0    gene_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; transcript_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; exon_number 3; 67 142 +
bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni    ALN     cds     6982    7119    271     +       0    gene_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; transcript_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; exon_number 4; 143 188 +
bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni    ALN     cds     8124    8275    301     +       0    gene_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; transcript_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; exon_number 5; 189 239 +
bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni    ALN     cds     8741    8865    255     +       1    gene_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; transcript_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; exon_number 6; 240 280 +
bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni    ALN     cds     9230    9376    280     +       2    gene_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; transcript_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; exon_number 7; 281 329 +
bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni    ALN     cds     9901    10096   168     +       2    gene_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; transcript_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; exon_number 8; 396 617 +
bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni    ALN     stop_codon      10096   10098   168     +    2gene_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni"; transcript_id "bmor_100037424_vacuolar_ATP_synthase_catalytic_subunit_A__K02145_V_type_H_transporting_ATPase_subuni";
bmor_100037426_enolase_EC_4_2_1_11___K01689_enolase_EC_4_2_1_11_A_      ALN     gene    1283    2581    1428    +       .       gene_id "bmor_100037426_enolase_EC_4_2_1_11___K01689_enolase_EC_4_2_1_11_A_"; transcript_id "bmor_100037426_enolase_EC_4_2_1_11___K01689_enolase_EC_4_2_1_11_A_"
bmor_100037426_enolase_EC_4_2_1_11___K01689_enolase_EC_4_2_1_11_A_      ALN     start_codon     1283    1285    1428    +       0       gene_id "bmor_100037426_enolase_EC_4_2_1_11___K01689_enolase_EC_4_2_1_11_A_"; transcript_id "bmor_100037426_enolase_EC_4_2_1_11___K01689_enolase_EC_4_2_1_11_A_";
bmor_100037426_enolase_EC_4_2_1_11___K01689_enolase_EC_4_2_1_11_A_      ALN     cds     1283    2581    1428    +       0       gene_id "bmor_100037426_enolase_EC_4_2_1_11___K01689_enolase_EC_4_2_1_11_A_"; transcript_id "bmor_100037426_enolase_EC_4_2_1_11___K01689_enolase_EC_4_2_1_11_A_"; exon_number 1; 1 433 +
bmor_100037426_enolase_EC_4_2_1_11___K01689_enolase_EC_4_2_1_11_A_      ALN     stop_codon      2581    2583    1428    +       0       gene_id "bmor_100037426_enolase_EC_4_2_1_11___K01689_enolase_EC_4_2_1_11_A_"; transcript_id "bmor_100037426_enolase_EC_4_2_1_11___K01689_enolase_EC_4_2_1_11_A_";
bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1    ALN     gene    975     3808    926     +       .    gene_id "bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1"; transcript_id "bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1"
bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1    ALN     start_codon     975     977     223     +    0gene_id "bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1"; transcript_id "bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1";
bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1    ALN     cds     975     1092    223     +       0    gene_id "bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1"; transcript_id "bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1"; exon_number 1; 1 39 +
bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1    ALN     cds     1465    1665    332     +       2    gene_id "bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1"; transcript_id "bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1"; exon_number 2; 40 106 +
bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1    ALN     cds     2207    2487    388     +       2    gene_id "bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1"; transcript_id "bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1"; exon_number 3; 107 200 +
bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1    ALN     cds     3713    3808    153     +       0    gene_id "bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1"; transcript_id "bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1"; exon_number 4; 201 233 +
bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1    ALN     stop_codon      3808    3810    153     +    0gene_id "bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1"; transcript_id "bmor_100037442_6pgl__6_phosphogluconolactonase_EC_3_1_1_31___K01057_6_phosphogluconolactonase_EC_3_1";
bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_    ALN     gene    1593    8843    2044    +       .    gene_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; transcript_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"
bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_    ALN     start_codon     1593    1595    93      +    0gene_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; transcript_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_";
bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_    ALN     cds     1593    1662    93      +       0    gene_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; transcript_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; exon_number 1; 1 22 +
bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_    ALN     cds     2381    2496    235     +       2    gene_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; transcript_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; exon_number 2; 23 61 +
bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_    ALN     cds     5305    5449    273     +       0    gene_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; transcript_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; exon_number 3; 62 109 +
bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_    ALN     cds     5741    5940    380     +       2    gene_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; transcript_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; exon_number 4; 110 176 +
bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_    ALN     cds     6262    6396    261     +       0    gene_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; transcript_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; exon_number 5; 177 221 +
bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_    ALN     cds     6487    6590    221     +       0    gene_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; transcript_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; exon_number 6; 222 256 +
bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_    ALN     cds     6717    6867    306     +       1    gene_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; transcript_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; exon_number 7; 257 306 +
bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_    ALN     cds     7709    7942    441     +       0    gene_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; transcript_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; exon_number 8; 307 384 +
bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_    ALN     cds     8694    8843    270     +       0    gene_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; transcript_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; exon_number 9; 385 435 +
bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_    ALN     stop_codon      8843    8845    270     +    0gene_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_"; transcript_id "bmor_100101164_NADPH_specific_isocitrate_dehydrogenase__K00031_isocitrate_dehydrogenase_EC_1_1_1_42_";
bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_    ALN     gene    784     1737    832     +       .    gene_id "bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_"; transcript_id "bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_"
bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_    ALN     start_codon     784     786     257     +    0gene_id "bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_"; transcript_id "bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_";
bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_    ALN     cds     784     902     257     +       0    gene_id "bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_"; transcript_id "bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_"; exon_number 1; 1 40 +
bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_    ALN     cds     1067    1285    359     +       1    gene_id "bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_"; transcript_id "bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_"; exon_number 2; 41 113 +
bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_    ALN     cds     1554    1737    320     +       1    gene_id "bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_"; transcript_id "bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_"; exon_number 3; 114 179 +
bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_    ALN     stop_codon      1737    1739    320     +    1gene_id "bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_"; transcript_id "bmor_100101181_H_transporting_ATP_synthase_subunit_d__K02138_F_type_H_transporting_ATPase_subunit_d_";
bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_        ALN     gene    344     7988    1378    +       .       gene_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; transcript_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"
bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_        ALN     start_codon     344     346     166     +       0    gene_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; transcript_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_";
bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_        ALN     cds     344     466     166     +       0       gene_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; transcript_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; exon_number 1; 1 41 +
bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_        ALN     cds     3280    3397    216     +       0       gene_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; transcript_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; exon_number 2; 42 80 +
bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_        ALN     cds     3474    3598    241     +       2       gene_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; transcript_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; exon_number 3; 81 122 +
bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_        ALN     cds     5378    5600    405     +       0       gene_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; transcript_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; exon_number 4; 123 196 +
bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_        ALN     cds     6809    7050    402     +       2       gene_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; transcript_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; exon_number 5; 197 277 +
bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_        ALN     cds     7827    7988    239     +       0       gene_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; transcript_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; exon_number 6; 278 331 +
bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_        ALN     stop_codon      7988    7990    239     +       0    gene_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_"; transcript_id "bmor_100124423_Ldh__lactate_dehydrogenase__K00016_L_lactate_dehydrogenase_EC_1_1_1_27_A_";
bmor_100127121_Uqcrc2__ubiquinol_cytochrome_c_reductase_core_protein_II_EC_1_10_2_2___K00415_ubiquin    ALN     gene    87      5318    1504    +       .    gene_id "bmor_100127121_Uqcrc2__ubiquinol_cytochrome_c_reductase_core_protein_II_EC_1_10_2_2___K00415_ubiquin"; transcript_id "bmor_100127121_Uqcrc2__ubiquinol_cytochrome_c_reductase_core_protein_II_EC_1_10_2_2___K00415_ubiquin"

What is the expected output?
don't know, but I do get some results.

What do you see instead?
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 31.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 31.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 41.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 41.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 52.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 52.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 73.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 73.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 114.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 114.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 116.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 116.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 31.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 31.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 41.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 41.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 52.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 52.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 73.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 73.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 114.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 114.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 116.
Argument "-" isn't numeric in subtraction (-) at /data/programs/popoolation_1.2.2/syn-nonsyn/../Modules/SynNonSyn.pm line 106, <$ifh> line 116.

What version of the product are you using? On what operating system?
popoolation_1.2.2/syn-nonsyn/Syn-nonsyn-at-position.p

Please provide any additional information below.