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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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Strange warnings from Shell script 2 #7

Closed jamespblloyd closed 6 years ago

jamespblloyd commented 7 years ago

Hey,

So I got a lot of strange warnings from running the second shell script. I am not sure what part is generating the warnings and how big a problem they are. But I do know that at the end of shell script 3 I get a LOT of errors and the final output files are nearly all empty. I am not sure if that problem is related to this or not but thought I would check what is is about (some of the whitespace has been removed from the warnings to make it easier to read).

bash /lab/app/JUM/JUM_170323/JUM_1.3.1/JUM_2.sh /lab/app/JUM/JUM_170323/JUM_1.3.1 5 2 150 Preparing for non-intron retention AS events analyses... 6 input samples for JUM analyses Preparing for intron retention AS events analyses... Processing junction overhangs for Sample S100... Success. Processing junction overhangs for Sample S104... Success. Processing junction overhangs for Sample S108... Success. Processing junction overhangs for Sample S102... Success.

*WARNING: -wb is ignored with -abam***WARNING: -wb is ignored with -abam **WARNING: -wb is ignored with -abam

WARNING: -wb is ignored with -abam

WARNING: -wb is ignored with -abam WARNING: -wb is ignored with -abam*****WARNING: -wb is ignored with -abam

WARNING: -wb is ignored with -abam **WARNING: -wb is ignored with -abam **WARNING: -wb is ignored with -abam*****

**WARNING: -wb is ignored with -abam

WARNING: -wb is ignored with -abam

ready to performing differential AS analyses... find: warning: you have specified the -maxdepth option after a non-option argument -type, but options are not positional (-maxdepth affects tests specified before it as well as those specified after it). Please specify options before other arguments.

Best, James

If it helps, the error message from shell script 3 is below: (It might be an issue with the process_raw_AS_differential_output.pl script but I do not know enough perl to comment on any further)

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 can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/process_raw_AS_differential_output.pl line 20. awk: cmd. line:1: fatal: cannot open file AS_differential.txt' for reading (No such file or directory) AS_differential.txt: No such file or directory AS_differential.txt: No such file or directory AS_differential.txt: No such file or directory Error: The requested bed file (temp_long_intron_retention_junction_coordinate_adjusted_pvalue_0.05.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_total.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_adjusted_pvalue_0.05.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_total.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_adjusted_pvalue_0.05.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_total.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_adjusted_pvalue_0.05.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_total.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_adjusted_pvalue_0.05.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_total.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_adjusted_pvalue_0.05.txt) could not be opened. Exiting! Error: The requested bed file (temp_long_intron_retention_junction_coordinate_total.txt) could not be opened. Exiting! Can't locate Array/Utils.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /lab/app/JUM/JUM_170323/JUM_1.3.1/screening_cassette_exon_events.pl line 4. BEGIN failed--compilation aborted at /lab/app/JUM/JUM_170323/JUM_1.3.1/screening_cassette_exon_events.pl line 4. Error: The requested bed file (cassette_exon_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open fileS100_temp_total_cassette_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (cassette_exon_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open file S104_temp_total_cassette_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (cassette_exon_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open fileS108_temp_total_cassette_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (cassette_exon_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open file S102_temp_total_cassette_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (cassette_exon_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open fileSC2_S106_temp_total_cassette_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (cassette_exon_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open file S110_temp_total_cassette_with_indicator.txt' for reading (No such file or directory) awk: cmd. line:1: fatal: cannot open filecassette_exon_coordinate.bed' for reading (No such file or directory) Can't locate Array/Utils.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /lab/app/JUM/JUM_170323/JUM_1.3.1/screening_MXE_events.pl line 4. BEGIN failed--compilation aborted at /lab/app/JUM/JUM_170323/JUM_1.3.1/screening_MXE_events.pl line 4. Error: The requested bed file (MXE_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open file S100_temp_total_MXE_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (MXE_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open fileS104_temp_total_MXE_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (MXE_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open file S108_temp_total_MXE_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (MXE_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open fileS102_temp_total_MXE_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (MXE_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open file S106_temp_total_MXE_with_indicator.txt' for reading (No such file or directory) Error: The requested bed file (MXE_coordinate.bed) could not be opened. Exiting! can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/count_intron_read_long_intron_retention_step2.pl line 17. can't open input1 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/determining_rightful_total_cassette_exon_event.pl line 17. awk: cmd. line:1: fatal: cannot open fileS110_temp_total_MXE_with_indicator.txt' for reading (No such file or directory) Can't locate Array/Utils.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /lab/app/JUM/JUM_170323/JUM_1.3.1/screening_A5SS_A3SS_events.pl line 4. BEGIN failed--compilation aborted at /lab/app/JUM/JUM_170323/JUM_1.3.1/screening_A5SS_A3SS_events.pl line 4. awk: cmd. line:1: fatal: cannot open file Valid_total_A5SS_event.txt' for reading (No such file or directory) can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/profiling_splicing_patterns_from_AS_events_4.pl line 18. awk: cmd. line:1: fatal: cannot open fileValid_total_A3SS_event.txt' for reading (No such file or directory) can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/profiling_splicing_patterns_from_AS_events_4.pl line 18. can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/profiling_splicing_patterns_from_AS_events_5.pl line 18. can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/profiling_splicing_patterns_from_AS_events_5.pl line 18. can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/profiling_splicing_patterns_from_AS_events_5.pl line 18. can't open input2 file: No such file or directory at /lab/app/JUM/JUM_170323/JUM_1.3.1/profiling_splicing_patterns_from_AS_events_6.pl line 20. mkdir: cannot create directory FINAL_JUM_OUTPUT': File exists mv: cannot statAS_differential_JUM_output_intron_retention_adjusted_pvalue_0.05.txt': No such file or directory mv: cannot stat `*coordinate.bed': No such file or directory

qqwang-berkeley commented 7 years ago

The warnings from running JUM_2.sh are all normal. No problem.

The warnings from running JUM_3.sh: it seems that you did not run the R script after running JUM_2.sh. The R_script_JUM.R will generate a file called AS_differential.txt which is needed for JUM_3.sh to run. You can take a look at the JUM manual again for details

jamespblloyd commented 7 years ago

Thanks for getting back to me!

Good to know that those warnings are normal for JUM_2.sh.

I did run the R script: Rscript /lab/app/JUM/JUM_170323/JUM_1.3.1/R_script_JUM.R experiment_design_pair1.txt > outputFile.Rout 2> errorFile.Rout

But there must have been a problem with either than or something regarding the input earlier. I will get back to you when I have investigated the problem further.

Edit: I looked in errorFile.Rout and I got this error message so perhaps it has something to do with DEXSeq not being able to install properly? I guess I will have to get R working properly. 

less errorFile.Rout
A new version of Bioconductor is available after installing the most
  recent version of R; see http://bioconductor.org/install
Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Installing package(s) 'DEXSeq'
trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/DEXSeq_1.4.0.tar.gz'
Content type 'application/x-gzip' length 314659 bytes (307 Kb)
opened URL
==================================================
downloaded 307 Kb

* installing *source* package ‘DEXSeq’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

* DONE (DEXSeq)
Warning message:
installed directory not writable, cannot update packages 'codetools',
  'colorspace', 'DBI', 'digest', 'gtable', 'hwriter', 'KernSmooth', 'labeling',
  'latticeExtra', 'matrixStats', 'mgcv', 'munsell', 'nnet', 'proto',
  'RColorBrewer', 'reshape2', 'R.methodsS3', 'rpart', 'scales', 'stringr',
  'survival', 'xtable'
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: methods

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

    xtabs

The following object(s) are masked from ‘package:base’:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
    get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Error: could not find function "DEXSeqDataSetFromHTSeq"
Execution halted