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qqwang-berkeley / JUM

A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns
MIT License
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Empty results of JUM_C.sh; lots of perl errors again #26

Closed acesnik closed 5 years ago

acesnik commented 5 years ago

Hi again,

I ran into another road block. I'm getting the scripts to run, but there are perl errors in both the outputs from JUM_B and JUM_C. I'll attach the logs here.

jum_b.log

The jum_c.log was too big to attach. This is the gist of it:

Smartmatch is experimental at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 55.
Smartmatch is experimental at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 55.
Use of uninitialized value $junctionID[10] in pattern match (m//) at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 50, <IN2> line 1.
Use of uninitialized value $junctionID[10] in pattern match (m//) at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 50, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 53, <IN2> line 1.
Use of uninitialized value $junctionID[10] in pattern match (m//) at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 50, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 53, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 53, <IN2> line 1.
Use of uninitialized value $junctionID[10] in pattern match (m//) at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 50, <IN2> line 1.
Use of uninitialized value $junctionID[10] in pattern match (m//) at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 50, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 53, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 53, <IN2> line 1.

^ that times 200M lines

Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 66, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 66, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 66, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_2.pl line 60.
Use of uninitialized value $array[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 27, <IN1> line 1.
Use of uninitialized value $temp[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_2.pl line 60.
Use of uninitialized value $array[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 27, <IN1> line 1.
Use of uninitialized value $temp[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_2.pl line 60.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_2.pl line 60.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_2.pl line 60.
Use of uninitialized value $array[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 27, <IN1> line 1.
Use of uninitialized value $temp[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value $array[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 27, <IN1> line 1.
Use of uninitialized value $temp[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value $array[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 27, <IN1> line 1.
Use of uninitialized value $temp[0] in hash element at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, <IN2> line 1.
Use of uninitialized value $array[11] in concatenation (.) or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 58, <IN1> line 1.
Use of uninitialized value in concatenation (.) or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 58, <IN1> line 1.
Use of uninitialized value in concatenation (.) or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 58, <IN1> line 1.
Use of uninitialized value in concatenation (.) or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 58, <IN1> line 1.
Use of uninitialized value in concatenation (.) or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 58, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 59, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 59, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 59, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 60, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 60, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 60, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 61, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 61, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 61, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value $pmin in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value $qmin in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 62, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_cassette_exon_output1.pl line 63, <IN1> line 1.
Use of uninitialized value $temp[1] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 30, <IN2> line 1.
Use of uninitialized value within @temp in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 58, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 58, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 58, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 59, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 59, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 59, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 60, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 60, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 60, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value $coor in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value $start in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value $end in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value $pmin in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value $qmin in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 61, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 62, <IN1> line 1.
Use of uninitialized value $coor in print at /home/tools/JUM_2.0.2/final_process_IR_output_long.pl line 62, <IN1> line 1.
Use of uninitialized value $array[0] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 23, <IN1> line 1.
Use of uninitialized value $temp[1] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 30, <IN2> line 1.
Use of uninitialized value within @temp in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value $temp[1] in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 46, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 47, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 48, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value $coor in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value $start in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value $end in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value $pmin in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value $qmin in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 49, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 50, <IN1> line 1.
Use of uninitialized value $coor in print at /home/tools/JUM_2.0.2/final_process_IR_output_short.pl line 50, <IN1> line 1.
Use of uninitialized value $array[0] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 23, <IN1> line 1.
Use of uninitialized value $temp[1] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 30, <IN2> line 1.
Use of uninitialized value within @temp in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value $temp[1] in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 74, <IN1> line 1.
Use of uninitialized value $as in string eq at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 74, <IN1> line 1.
Use of uninitialized value $lineid in hash element at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 75, <IN1> line 1.
Use of uninitialized value $lineid in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 76, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 191, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 199, <IN1> line 1.
Use of uninitialized value $i in numeric le (<=) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 202, <IN1> line 1.
Use of uninitialized value $unique_id[0] in sort at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 215, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 218, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 219, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 220, <IN1> line 1.
Use of uninitialized value $as in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 221, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 222, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 222, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 222, <IN1> line 1.
Use of uninitialized value $sorted_id[-1] in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 226, <IN1> line 1.
Use of uninitialized value $gene in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 228, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 228, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 228, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 228, <IN1> line 1.
Use of uninitialized value $sorted_id[-1] in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 232, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 233, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 233, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 233, <IN1> line 1.
Use of uninitialized value within @sorted_id in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 237, <IN1> line 1.
Use of uninitialized value in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 237, <IN1> line 1.
Use of uninitialized value $sorted_id[-1] in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 238, <IN1> line 1.
Use of uninitialized value $pmin in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 239, <IN1> line 1.
Use of uninitialized value $qmin in print at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 239, <IN1> line 1.
Use of uninitialized value $i in subtraction (-) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 241, <IN1> line 1.
Use of uninitialized value in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 259, <IN1> line 1.
Use of uninitialized value in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 259, <IN1> line 1.
Use of uninitialized value in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 259, <IN1> line 1.
Use of uninitialized value in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 262, <IN1> line 1.
Use of uninitialized value in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 262, <IN1> line 1.
Use of uninitialized value in addition (+) at /home/tools/JUM_2.0.2/final_process_MXE_output.pl line 262, <IN1> line 1.
Use of uninitialized value $temp[1] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 30, <IN2> line 1.
Use of uninitialized value within @temp in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 64, <IN1> line 1.
Use of uninitialized value $as in string eq at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 64, <IN1> line 1.
Use of uninitialized value $strand in string eq at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 65, <IN1> line 1.
Use of uninitialized value $strand in string eq at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 65, <IN1> line 1.
Use of uninitialized value $unique_id[0] in sort at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 125, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 126, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 127, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 128, <IN1> line 1.
Use of uninitialized value $as in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 129, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in join or string at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $gene in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in join or string at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $common3prime in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $a5ss[0] in join or string at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $pmin in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 132, <IN1> line 1.
Use of uninitialized value $qmin in print at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 132, <IN1> line 1.
Use of uninitialized value $dpsi[0] in join or string at /home/tools/JUM_2.0.2/final_process_A5SS_output.pl line 133, <IN1> line 1.
Use of uninitialized value $temp[1] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 30, <IN2> line 1.
Use of uninitialized value within @temp in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 64, <IN1> line 1.
Use of uninitialized value $as in string eq at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 64, <IN1> line 1.
Use of uninitialized value $strand in string eq at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 65, <IN1> line 1.
Use of uninitialized value $strand in string eq at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 65, <IN1> line 1.
Use of uninitialized value $unique_id[0] in sort at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 124, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 125, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 126, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 127, <IN1> line 1.
Use of uninitialized value $as in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 128, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 129, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 129, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in join or string at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 129, <IN1> line 1.
Use of uninitialized value $gene in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in join or string at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $common5prime in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $a3ss[0] in join or string at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 130, <IN1> line 1.
Use of uninitialized value $pmin in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $qmin in print at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 131, <IN1> line 1.
Use of uninitialized value $dpsi[0] in join or string at /home/tools/JUM_2.0.2/final_process_A3SS_output.pl line 132, <IN1> line 1.
Use of uninitialized value $temp[1] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 30, <IN2> line 1.
Use of uninitialized value within @temp in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.
Use of uninitialized value in string eq at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 54, <IN1> line 1.
Use of uninitialized value $as in string eq at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 54, <IN1> line 1.
Use of uninitialized value $unique_id[0] in sort at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 99, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 100, <IN1> line 1.
Use of uninitialized value $_ in substitution (s///) at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 101, <IN1> line 1.
Use of uninitialized value in subroutine entry at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 102, <IN1> line 1.
Use of uninitialized value $as in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 103, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 104, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 104, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in join or string at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 104, <IN1> line 1.
Use of uninitialized value $gene in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in join or string at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $chr in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $strand in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $sorted_id[0] in join or string at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 105, <IN1> line 1.
Use of uninitialized value $pmin in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 106, <IN1> line 1.
Use of uninitialized value $qmin in print at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 106, <IN1> line 1.
Use of uninitialized value $dpsi[0] in join or string at /home/tools/JUM_2.0.2/final_process_composite_output.pl line 107, <IN1> line 1.
Use of uninitialized value $temp[1] in hash element at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 30, <IN2> line 1.
Use of uninitialized value within @temp in join or string at /home/tools/JUM_2.0.2/final_process_cassette_exon_output2.pl line 32, <IN2> line 1.

Here are the commands I used:

JUM_B.sh command cd output/JUM_Analysis/JUM_diff && (../../../tools/JUM_2.0.2/JUM_B.sh --Folder $(readlink -f ../../../tools/JUM_2.0.2/) --Test pvalue --Cutoff 1 --TotalFileNum 6 --Condition1SampleName G1_1.,G1_2.,G1_3. --Condition2SampleName S_1.,S_2.,S_3. --Condition1_fileNum_threshold 2 --Condition2_fileNum_threshold 2) 2> ../../jum_b.log && cd ../../..

JUM_C command cd output/JUM_Analysis/JUM_diff/FINAL_JUM_OUTPUT_pvalue_1 && (../../../../tools/JUM_2.0.2/JUM_C.sh --Folder $(readlink -f ../../../../tools/JUM_2.0.2/) --Test pvalue --Cutoff 1 --TotalCondition1FileNum 3 --TotalCondition2FileNum 3 --REF ../../../../ensembl/Homo_sapiens.GRCh38.96.gff3.refflat.fi x.txt) 2> ../../../jum_c.log && cd ../../../..

Some of the output files have weird stuff like __ARRAY(0x7fffebd2d1e0)___ written in them:

AS_differential_JUM_output_cassette_exon_events_pvalue_1_final_detailed.txt

acesnik commented 5 years ago

Here's a chunk of the refflat file:

gene:ENSG00000172288    transcript:ENST00000306609  Y   +   25622161    25624902    25622442    25624527    2   25622161,25624454,  25624034,25624902,
gene:ENSG00000172288    transcript:ENST00000361963  Y   +   25622161    25624338    25622442    25624065    1   25622161,   25624338,
gene:ENSG00000185894    transcript:ENST00000602680  Y   -   25043990    25062548    25043990    25044023    5   25043990,25048473,25051675,25052150,25062392,   25044064,25048610,25051798,25052219,25062548,
gene:ENSG00000185894    transcript:ENST00000618574  Y   -   25038097    25044023    25038097    25044023    4   25038097,25038808,25041768,25043945,    25038116,25038914,25041886,25044023,
gene:ENSG00000185894    transcript:ENST00000382287  Y   -   25030900    25052104    25038097    25044023    9   25030900,25031316,25037991,25038808,25041768,25043945,25048473,25051675,25052073,   25031222,25031441,25038116,25038914,25041886,25044064,25048610,25051798,25052104,
gene:ENSG00000205916    transcript:ENST00000382296  Y   +   24834126    24905240    24834126    24901175    26  24834126,24840730,24841151,24841803,24842291,24842444,24851578,24851999,24852651,24853139,24853292,24854832,24857275,24859665,24862061,24864445,24866841,24869218,24871598,24873975,24883763,24893302,24895687,24896504,24901111,24905183,  24834129,24840877,24841243,24841855,24842355,24842584,24851725,24852091,24852703,24853203,24853432,24854904,24857347,24859737,24862133,24864517,24866913,24869290,24871670,24874047,24883835,24893374,24895759,24896539,24901210,24905240,
acesnik commented 5 years ago

Okay, it turns out I didn't follow this step. I didn't make the experimental_design.txt file or run the Rscript.

image

After doing that, it ran through the end.

acesnik commented 5 years ago

Ideally, it should check for the files and throw an error if they're not there. That'd have saved some time. :)