So I think I have a bug to report. I ran the R script (successfully I think) and generated a lot of scripts from this. However, when I run the third shell script, I get an error for a missing file (AS_differential_JUM_output_intron_retention_adjusted_pvalue_0.05.txt). I can find many files with a similar name but not this one. Is there a bug with making a file with this name or did I run something incorrectly. Please see the commands and files below.
bash /lab/app/JUM/JUM_170323/JUM_1.3.1/JUM_3.sh /lab/app/JUM/JUM_170323/JUM_1.3.1 adjusted_pvalue 0.05 6 3 Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. mv: cannot statAS_differential_JUM_output_intron_retention_adjusted_pvalue_0.05.txt': No such file or directory`
The last line seems to be the most informative about what went wrong. I looked to see if I had this file but I do not, instead I have some with a similar name but without the JUMoutput
Hello,
So I think I have a bug to report. I ran the R script (successfully I think) and generated a lot of scripts from this. However, when I run the third shell script, I get an error for a missing file (AS_differential_JUM_output_intron_retention_adjusted_pvalue_0.05.txt). I can find many files with a similar name but not this one. Is there a bug with making a file with this name or did I run something incorrectly. Please see the commands and files below.
bash /lab/app/JUM/JUM_170323/JUM_1.3.1/JUM_3.sh /lab/app/JUM/JUM_170323/JUM_1.3.1 adjusted_pvalue 0.05 6 3 Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 261. Use of uninitialized value in print at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 47, <IN2> line 505. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. Use of uninitialized value $_ in pattern match (m//) at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 52. mv: cannot statAS_differential_JUM_output_intron_retention_adjusted_pvalue_0.05.txt': No such file or directory`The last line seems to be the most informative about what went wrong. I looked to see if I had this file but I do not, instead I have some with a similar name but without the JUMoutput
ls -lh *AS_differential*intron* -rw-r--r-- 1 jamesl lab 2.2K Apr 11 17:26 AS_differential_adjusted_pvalue_0.05_long_intron_retention_passing_filter_combined_list.txt -rw-r--r-- 1 jamesl lab 13K Apr 11 17:18 AS_differential_adjusted_pvalue_0.05_non_intron_retention_AS_structure_list.txt -rw-r--r-- 1 jamesl lab 2.2K Apr 11 17:26 AS_differential_adjusted_pvalue_0.05_valid_long_intron_retention_list.txt -rw-r--r-- 1 jamesl lab 148 Apr 11 17:18 AS_differential_adjusted_pvalue_0.05_valid_short_intron_retention_list.txt -rw-r--r-- 1 jamesl lab 11K Apr 11 17:26 AS_differential_total_long_intron_retention_passing_filter_combined_list.txt -rw-r--r-- 1 jamesl lab 11K Apr 11 17:26 AS_differential_total_valid_long_intron_retention_list.txt -rw-r--r-- 1 jamesl lab 7.4K Apr 11 17:18 AS_differential_total_valid_short_intron_retention_list.txt