RSEQREP *.sh file error

[ngs-dnax]

I am tired to run RSEQREP on local Ubuntu server.RSEQREP AWS AMI,RSEQREP Docker Image. sh setup.sh Loading required package: methods Performing sanity checks on configuration options Parsing Analysis Configuration Parsing Sample Metadata Parsing Workflow Configuration Preparing GSEA Gene Sets Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 3 elements Calls: getBM -> read.table -> scan Execution halted sh run-all.sh Loading required package: methods Performing sanity checks on configuration options Parsing Analysis Configuration Parsing Sample Metadata Parsing Workflow Configuration Preparing GSEA Gene Sets Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 3 elements Calls: getBM -> read.table -> scan Execution halted head: cannot open '/home/dnax/Downloads/emmesgit-RSEQREP-fc7e8ff/ubuntu/RSEQREP/source/../dir.csv' for reading: No such file or directory head: cannot open '/home/dnax/Downloads/emmesgit-RSEQREP-fc7e8ff/ubuntu/RSEQREP/source/../dir.csv' for reading: No such file or directory head: cannot open '/home/dnax/Downloads/emmesgit-RSEQREP-fc7e8ff/ubuntu/RSEQREP/source/../dir.csv' for reading: No such file or directory tail: cannot open '/home/dnax/Downloads/emmesgit-RSEQREP-fc7e8ff/ubuntu/RSEQREP/source/../dir.csv' for reading: No such file or directory mkdir: cannot create directory ‘/root/.ncbi’: File exists cd perl /home/dnax/Downloads/emmesgit-RSEQREP-fc7e8ff/ubuntu/RSEQREP/source/perl/preprocess-rnaseq.pl
Use of uninitialized value $worklowConfigFile in open at /home/dnax/Downloads/emmesgit-RSEQREP-fc7e8ff/ubuntu/RSEQREP/source/perl/preprocess-rnaseq.pl line 55. Cannot open workflow configuration file: No such file or directory at /home/dnax/Downloads/emmesgit-RSEQREP-fc7e8ff/ubuntu/RSEQREP/source/perl/preprocess-rnaseq.pl line 55. Creating Feature Counts Matrix... run-all.sh: 83: run-all.sh: cannot create /data/fragment_count_matrix.tab: Directory nonexistent gzip: /data/fragment_count_matrix.tab: No such file or directory Creating Read Distribution Matrix... run-all.sh: 90: run-all.sh: cannot create /rseqc/bam_rc_parsed.tab: Directory nonexistent find: ‘/rseqc/bam_rc_parsed.tab’: No such file or directory Creating BAM GC Matrix... run-all.sh: 97: run-all.sh: cannot create /rseqc/bam_gc_parsed.tab: Directory nonexistent Creating BAM JC Matrix... run-all.sh: 103: run-all.sh: cannot create /rseqc/bam_jc_parsed.tab: Directory nonexistent Creating BAM QC Matrix... run-all.sh: 109: run-all.sh: cannot create /rseqc/bam_qc_parsed.tab: Directory nonexistent Error in setwd(dta.dir) : cannot change working directory Execution halted Loading required package: edgeR Loading required package: biomaRt Loading required package: methods Loading required package: goseq Loading required package: BiasedUrn Loading required package: geneLenDataBase

Loading required package: xtable Loading required package: MASS

Attaching package: ‘MASS’

The following object is masked from ‘package:biomaRt’:

select

Loading required package: gplots Loading required package: sqldf Loading required package: pvclust Loading required package: car Loading required package: knitr Loading required package: vegan Loading required package: R.utils Loading required package: gtools Loading required package: stringr Loading required package: plyr Loading required package: grid Loading required package: gridExtra Loading required package: UpSetR Loading required package: Cairo Error in file(file, "rt") : cannot open the connection Calls: source ... withVisible -> eval -> eval -> read.csv -> read.table -> file In addition: There were 14 warnings (use warnings() to see them) Execution halted Loading required package: edgeR Loading required package: biomaRt Loading required package: methods Loading required package: goseq Loading required package: BiasedUrn Loading required package: geneLenDataBase

Loading required package: xtable Loading required package: MASS

Attaching package: ‘MASS’

The following object is masked from ‘package:biomaRt’:

select

Loading required package: gplots Loading required package: sqldf Loading required package: pvclust Loading required package: car Loading required package: knitr Loading required package: vegan Loading required package: R.utils Loading required package: gtools Loading required package: stringr Loading required package: plyr Loading required package: grid Loading required package: gridExtra Loading required package: UpSetR Loading required package: Cairo Error in file(file, "rt") : cannot open the connection Calls: source ... withVisible -> eval -> eval -> read.csv -> read.table -> file In addition: There were 14 warnings (use warnings() to see them) Execution halted Loading required package: edgeR Loading required package: biomaRt Loading required package: methods Loading required package: goseq Loading required package: BiasedUrn Loading required package: geneLenDataBase

Loading required package: xtable Loading required package: MASS

Attaching package: ‘MASS’

The following object is masked from ‘package:biomaRt’:

select

Loading required package: gplots Loading required package: sqldf Loading required package: pvclust Loading required package: car Loading required package: knitr Loading required package: vegan Loading required package: R.utils Loading required package: gtools Loading required package: stringr Loading required package: plyr Loading required package: grid Loading required package: gridExtra Loading required package: UpSetR Loading required package: Cairo Error in file(file, "rt") : cannot open the connection Calls: source ... withVisible -> eval -> eval -> read.csv -> read.table -> file In addition: There were 14 warnings (use warnings() to see them) Execution halted Loading required package: edgeR Loading required package: biomaRt Loading required package: methods Loading required package: edgeR Loading required package: biomaRt Loading required package: methods Loading required package: edgeR Loading required package: biomaRt Loading required package: methods Loading required package: goseq Loading required package: BiasedUrn Loading required package: geneLenDataBase Loading required package: goseq Loading required package: BiasedUrn Loading required package: geneLenDataBase Loading required package: goseq Loading required package: BiasedUrn Loading required package: geneLenDataBase

Loading required package: xtable Loading required package: MASS

Attaching package: ‘MASS’

The following object is masked from ‘package:biomaRt’:

select

Loading required package: gplots Loading required package: sqldf Loading required package: pvclust Loading required package: car Loading required package: knitr Loading required package: vegan Loading required package: R.utils Loading required package: gtools Loading required package: stringr Loading required package: plyr Loading required package: grid Loading required package: gridExtra Loading required package: UpSetR Loading required package: Cairo Error in file(file, "rt") : cannot open the connection Calls: source ... withVisible -> eval -> eval -> read.csv -> read.table -> file In addition: There were 14 warnings (use warnings() to see them) Execution halted

Loading required package: xtable Loading required package: MASS

Attaching package: ‘MASS’

The following object is masked from ‘package:biomaRt’:

select

Loading required package: gplots Loading required package: sqldf Loading required package: pvclust Loading required package: car Loading required package: knitr Loading required package: vegan Loading required package: R.utils Loading required package: gtools Loading required package: stringr Loading required package: plyr Loading required package: grid Loading required package: gridExtra Loading required package: UpSetR Loading required package: Cairo Error in file(file, "rt") : cannot open the connection Calls: source ... withVisible -> eval -> eval -> read.csv -> read.table -> file In addition: There were 14 warnings (use warnings() to see them) Execution halted

Loading required package: xtable Loading required package: MASS

Attaching package: ‘MASS’

The following object is masked from ‘package:biomaRt’:

select

Loading required package: gplots Loading required package: sqldf Loading required package: pvclust Loading required package: car Loading required package: knitr Loading required package: vegan Loading required package: R.utils Loading required package: gtools Loading required package: stringr Loading required package: plyr Loading required package: grid Loading required package: gridExtra Loading required package: UpSetR Loading required package: Cairo Error in file(file, "rt") : cannot open the connection Calls: source ... withVisible -> eval -> eval -> read.csv -> read.table -> file In addition: There were 14 warnings (use warnings() to see them) Execution halted Loading required package: edgeR Loading required package: biomaRt Loading required package: methods Loading required package: goseq Loading required package: BiasedUrn Loading required package: geneLenDataBase

Loading required package: xtable Loading required package: MASS

Attaching package: ‘MASS’

The following object is masked from ‘package:biomaRt’:

select

Loading required package: gplots Loading required package: sqldf Loading required package: pvclust Loading required package: car Loading required package: knitr Loading required package: vegan Loading required package: R.utils Loading required package: gtools Loading required package: stringr Loading required package: plyr Loading required package: grid Loading required package: gridExtra Loading required package: UpSetR Loading required package: Cairo Error in file(file, "rt") : cannot open the connection Calls: source ... withVisible -> eval -> eval -> read.csv -> read.table -> file In addition: There were 14 warnings (use warnings() to see them) Execution halted Loading required package: edgeR Loading required package: biomaRt Loading required package: methods Loading required package: goseq Loading required package: BiasedUrn Loading required package: geneLenDataBase

Loading required package: xtable Loading required package: MASS

Attaching package: ‘MASS’

The following object is masked from ‘package:biomaRt’:

select

Loading required package: gplots Loading required package: sqldf Loading required package: pvclust Loading required package: car Loading required package: knitr Loading required package: vegan Loading required package: R.utils Loading required package: gtools Loading required package: stringr Loading required package: plyr Loading required package: grid Loading required package: gridExtra Loading required package: UpSetR Loading required package: Cairo Error in file(file, "rt") : cannot open the connection Calls: source ... withVisible -> eval -> eval -> read.csv -> read.table -> file In addition: There were 14 warnings (use warnings() to see them) Execution halted Loading required package: edgeR Loading required package: biomaRt Loading required package: methods Loading required package: goseq Loading required package: BiasedUrn Loading required package: geneLenDataBase

Loading required package: xtable Loading required package: MASS

Attaching package: ‘MASS’

The following object is masked from ‘package:biomaRt’:

select

Loading required package: gplots Loading required package: sqldf Loading required package: pvclust Loading required package: car Loading required package: knitr Loading required package: vegan Loading required package: R.utils Loading required package: gtools Loading required package: stringr Loading required package: plyr Loading required package: grid Loading required package: gridExtra Loading required package: UpSetR Loading required package: Cairo Error in file(file, "rt") : cannot open the connection Calls: source ... withVisible -> eval -> eval -> read.csv -> read.table -> file In addition: There were 14 warnings (use warnings() to see them) Execution halted rm: cannot remove '/report/cache/': No such file or directory rm: cannot remove '/report/figs/': No such file or directory rm: cannot remove '/report/tables/': No such file or directory Error in setwd("/report") : cannot change working directory Execution halted run-all.sh: 151: cd: can't cd to /report This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode ! I can't find file `rseq-report.tex'. <> rseq-report.tex

(Press Enter to retry, or Control-D to exit) Please type another input file name: ^C! I can't find file `rseq-report.tex'. <*> rseq-report.tex

(Press Enter to retry, or Control-D to exit) Please type another input file name: ^C^C^C^C ! Emergency stop. <*> rseq-report.tex

! ==> Fatal error occurred, no output PDF file produced! Transcript written on texput.log. PLEASE HELP ASAP !!!

[emmesgit]

Since I do not have access to the configuration log you used, I can only make a best guess. The first error comes from the configuration parsing script (parse-rnaseq-configuration.r) which is unable to create the gene set enrichment files: "Preparing GSEA Gene Sets Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 3 elements Calls: getBM -> read.table -> scan Execution halted"

This has kept important out files from being written.
1) please ensure that the "gmt_entrez_files" and "gmt_entrez_files_labels" variables in the excel configuration file (config.xlsx) workflow_config tab are either filled out with valid file names or completely empty. 2) Please take a look at your RSEQREP version -- are you running the latest version of the software? A bug fix on these fields was made in a recent version.

Hopefully this helps.

Best, -Travis

[ngs-dnax]

Thanku sir my config file configq.xlsx config.xlsx we choose both config file but both have same error found and also i used RSEQREP version --1.1.2

[emmesgit]

Thank you for providing the configuration file you are using -- This is helpful. Considering there have been several bug fixes since v1.1.2, I would first recommend updating RSEQREP as a whole to the current version (especially since there has been a bug fix in the fields that are causing issues). The configuration file MUST be named config.xlsx and it must be located at RSEQREP/config/config.xlsx. I noticed a number of other issues in your configuration file:

in the workflow_config tab: these fields must have a valid value: run_read_dist, stranded, all of the *_prog fields, and save_cram.

in the analysis_config tab: the seed must be a whole number (date usually works well ie: 20181002), outliers should only include samples with an outlying profile (generally you would find these in the PCA/MDS/HCL plots in the report after the first time you run the full analysis), so based on your configuration setup, I would not expect to see any outliers -- this can be left blank. prior_count can likely be set to 0.5 to avoid taking the log of 0 upon log transformation of feature counts data. all empty fields in the analysis_config tab should have values set -- try starting with the values set in the henn et. al. configuration file. heatmap_lfc_cols must be hex values (again, see the henn et. al. configuration file), glm_model_lfc_cutoff should be closer to something like 1.5 (this indicates a fold change of >=1.5 and <=-1.5).

please be sure to adhere to the field requirements in the Description filed in each tab -- using the henn et. al. configuration file as an example for each field.

best, -Travis