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Hello GiantSpaceRobot
I can successfully run the group comparison analysis with your example file results, when I try to do the group comparison analysis based on our own data , I always meet Error executing process > 'BARPLOTS'.
can you help me to solve this issue?

executor > local (46)
[8c/8b9bf0] process > PREPARE_TRNA_GTF [100%] 1 of 1 ✔
[86/d7cf71] process > PREPARE_NCRNA_GTF [100%] 1 of 1 ✔
[be/6bb898] process > TRIM_READS (2) [100%] 2 of 2 ✔
[99/efe468] process > MAKE_STAR_DB [100%] 1 of 1 ✔
[1a/d89db6] process > STAR_ALIGN (2) [100%] 2 of 2 ✔
[20/5a4419] process > BAM_COLLAPSE (2) [100%] 2 of 2 ✔
[5c/bdc724] process > ADD_EMPTY_COUNTS (B14_1_L3_... [100%] 2 of 2 ✔
[73/d6e37c] process > BAM_SPLIT (2) [100%] 2 of 2 ✔
[e9/70ec03] process > FEATURE_COUNT_TRNA (B14_1_L... [100%] 2 of 2 ✔
[ae/030849] process > FEATURE_COUNT_NCRNA (B14_1_... [100%] 2 of 2 ✔
[ab/9b0c9b] process > SUM_COUNTS [100%] 1 of 1 ✔
[3f/d270fe] process > GENERATE_TRNA_DEPTH_FILES (... [100%] 2 of 2 ✔
[06/c0a6ce] process > GENERATE_MULTIMAPPER_TRNA_D... [100%] 2 of 2 ✔
[e1/bfde3b] process > GENERATE_NCRNA_DEPTH_FILES ... [100%] 2 of 2 ✔
[68/9e3b51] process > GENERATE_DEPTHFILE_STATS (B... [100%] 4 of 4 ✔
[18/1a499e] process > RAW_COUNTS_TO_PROPORTIONS (... [100%] 2 of 2 ✔
[fb/af50b8] process > RAW_COUNTS_TO_NORM_COUNTS (... [100%] 2 of 2 ✔
[2e/ba7d5c] process > COUNTS_TO_COLLAPSED_COUNTS ... [100%] 4 of 4 ✔
[26/2926af] process > PREDICT_TSRNA_TYPE [100%] 1 of 1 ✔
[78/45980d] process > PLOT_TRNA_ALIGNMENT_LENGTH ... [ 50%] 1 of 2
[3c/223f44] process > PLOT_TRNA_ALL_PLOTS (B14_1_... [100%] 2 of 2 ✔
[- ] process > GENERATE_RESULTS_PDF -
[a9/eff521] process > DESEQ2 [ 0%] 0 of 1
[36/7e4bf3] process > DATA_TRANSFORMATIONS [ 0%] 0 of 1
[- ] process > DISTRIBUTION_SCORE -
[- ] process > SLOPE_SCORE -
[- ] process > CLEAVAGE_SCORE -
[- ] process > FISHERS_METHOD -
[- ] process > RESULTS_TABLE -
[- ] process > COMBINED_SCORE -
[- ] process > PLOT_TSRNA_LENGTHS -
[- ] process > PLOT_TRNAS -
[- ] process > PLOT_NCRNAS -
[- ] process > VENN_DIAGRAM -
[29/e3ed1a] process > GENERATE_COUNT_DATAFRAME [100%] 1 of 1 ✔
[9e/6ff258] process > STACKED_BARPLOTS [100%] 1 of 1 ✔
[86/17119b] process > BARPLOTS [ 0%] 0 of 1
[- ] process > PREDICT_TSRNA_TYPE_GROUPS -
[- ] process > GENERATE_RESULTS_PDF_GROUPS -
[- ] process > ORGANISE_RESULTS_GROUPS -
[- ] process > PUBLISH_FILES -
Error executing process > 'BARPLOTS'

Caused by:
Process BARPLOTS terminated with an error exit status (1)

Command executed:

Barplots.R
All-Features_raw-counts.tsv
human_ncRNAs_relative_cdhit.gtf
Layout.csv

Command exit status:
1

Command output:
(empty)

Command error:
Note: Using an external vector in selections is ambiguous.
ℹ Use all_of(ReplicateNumber1) instead of ReplicateNumber1 to silence this message.
ℹ See https://tidyselect.r-lib.org/reference/faq-external-vector.html.
This message is displayed once per session.
Error in t.test.default(my.column.condition1, my.column.condition2) :
not enough 'x' observations
Calls: t.test -> t.test.default
Execution halted

Work dir:
/lustre/wangzh/SC/tsrna_test/combinde_test/work/86/17119be4163e8ce0eeecd1b20aab30

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

WARN: Killing pending tasks (3)

executor > local (46)
[8c/8b9bf0] process > PREPARE_TRNA_GTF [100%] 1 of 1 ✔
[86/d7cf71] process > PREPARE_NCRNA_GTF [100%] 1 of 1 ✔
[be/6bb898] process > TRIM_READS (2) [100%] 2 of 2 ✔
[99/efe468] process > MAKE_STAR_DB [100%] 1 of 1 ✔
[1a/d89db6] process > STAR_ALIGN (2) [100%] 2 of 2 ✔
[20/5a4419] process > BAM_COLLAPSE (2) [100%] 2 of 2 ✔
[5c/bdc724] process > ADD_EMPTY_COUNTS (B14_1_L3_... [100%] 2 of 2 ✔
[73/d6e37c] process > BAM_SPLIT (2) [100%] 2 of 2 ✔
[e9/70ec03] process > FEATURE_COUNT_TRNA (B14_1_L... [100%] 2 of 2 ✔
[ae/030849] process > FEATURE_COUNT_NCRNA (B14_1_... [100%] 2 of 2 ✔
[ab/9b0c9b] process > SUM_COUNTS [100%] 1 of 1 ✔
[3f/d270fe] process > GENERATE_TRNA_DEPTH_FILES (... [100%] 2 of 2 ✔
[06/c0a6ce] process > GENERATE_MULTIMAPPER_TRNA_D... [100%] 2 of 2 ✔
[e1/bfde3b] process > GENERATE_NCRNA_DEPTH_FILES ... [100%] 2 of 2 ✔
[68/9e3b51] process > GENERATE_DEPTHFILE_STATS (B... [100%] 4 of 4 ✔
[18/1a499e] process > RAW_COUNTS_TO_PROPORTIONS (... [100%] 2 of 2 ✔
[fb/af50b8] process > RAW_COUNTS_TO_NORM_COUNTS (... [100%] 2 of 2 ✔
[2e/ba7d5c] process > COUNTS_TO_COLLAPSED_COUNTS ... [100%] 4 of 4 ✔
[26/2926af] process > PREDICT_TSRNA_TYPE [100%] 1 of 1 ✔
[78/45980d] process > PLOT_TRNA_ALIGNMENT_LENGTH ... [100%] 1 of 1
[3c/223f44] process > PLOT_TRNA_ALL_PLOTS (B14_1_... [100%] 2 of 2 ✔
[- ] process > GENERATE_RESULTS_PDF -
[- ] process > DESEQ2 -
[- ] process > DATA_TRANSFORMATIONS -
[- ] process > DISTRIBUTION_SCORE -
[- ] process > SLOPE_SCORE -
[- ] process > CLEAVAGE_SCORE -
[- ] process > FISHERS_METHOD -
[- ] process > RESULTS_TABLE -
[- ] process > COMBINED_SCORE -
[- ] process > PLOT_TSRNA_LENGTHS -
[- ] process > PLOT_TRNAS -
[- ] process > PLOT_NCRNAS -
[- ] process > VENN_DIAGRAM -
[29/e3ed1a] process > GENERATE_COUNT_DATAFRAME [100%] 1 of 1 ✔
[9e/6ff258] process > STACKED_BARPLOTS [100%] 1 of 1 ✔
[86/17119b] process > BARPLOTS [100%] 1 of 1, failed: 1 ✘
[- ] process > PREDICT_TSRNA_TYPE_GROUPS -
[- ] process > GENERATE_RESULTS_PDF_GROUPS -
[- ] process > ORGANISE_RESULTS_GROUPS -
[- ] process > PUBLISH_FILES -
Error executing process > 'BARPLOTS'

Caused by:
Process BARPLOTS terminated with an error exit status (1)

Command executed:

Barplots.R
All-Features_raw-counts.tsv
human_ncRNAs_relative_cdhit.gtf
Layout.csv

Command exit status:
1

Command output:
(empty)

Command error:
Note: Using an external vector in selections is ambiguous.
ℹ Use all_of(ReplicateNumber1) instead of ReplicateNumber1 to silence this message.
ℹ See https://tidyselect.r-lib.org/reference/faq-external-vector.html.
This message is displayed once per session.
Error in t.test.default(my.column.condition1, my.column.condition2) :
not enough 'x' observations
Calls: t.test -> t.test.default
Execution halted

Work dir:
/lustre/wangzh/SC/tsrna_test/combinde_test/work/86/17119be4163e8ce0eeecd1b20aab30

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

Hello GiantSpaceRobot
tsRNAsearch is a very amazing tool for tRNA mapping, but whether tsRNAsearch is suitable for paired-end RNA-seq data ?

I have noticed that this sometimes fails, most likely due to pre-existing software conflicts. One solution is to run the installation of R packages twice:
Rscript tsRNAsearch/bin/InstallPackages.R

Seems like there is an error with PLOT_TRNA_ALIGNMENT_LENGTH:

Error executing process > 'PLOT_TRNA_ALIGNMENT_LENGTH (trimmed_19101-0003_SmallRNA_accepted_hits_tRNAs).

The full error is copy pasted below:

Error executing process > 'PLOT_TRNA_ALIGNMENT_LENGTH (trimmed_19101-0003_SmallRNA_accepted_hits_tRNAs)'

Caused by:
Process PLOT_TRNA_ALIGNMENT_LENGTH (trimmed_19101-0003_SmallRNA_accepted_hits_tRNAs) terminated with an error exit status (1)

Command executed:

samtools view -h -o trimmed_19101-0003_SmallRNA_accepted_hits_tRNAs.sam trimmed_19101-0003_SmallRNA_accepted_hits_tRNAs.bam
grep -v ^@ trimmed_19101-0003_SmallRNA_accepted_hits_tRNAs.sam > trimmed_19101-0003_SmallRNA_accepted_hits_tRNAs_no-header.sam
tRNA_Alignment_Length.R \
trimmed_19101-0003_SmallRNA_accepted_hits_tRNAs_no-header.sam \
trimmed_19101-0003_SmallRNA_accepted_hits_tRNAs_tRNA-alignment-length
rm trimmed_19101-0003_SmallRNA_accepted_hits_tRNAs.sam trimmed_19101-0003_SmallRNA_accepted_hits_tRNAs_no-header.sam
for i in trimmed_accepted; do
mv $i $(echo $i | sed 's/_trimmed_accepted_hits_tRNAs//g')
done

Command exit status:
1

Command output:
null device
1

Command error:
Warning message:
replacing previous import ‘vctrs::data_frame’ by ‘tibble::data_frame’ when loading ‘dplyr’

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

  filter, lag

The following objects are masked from ‘package:base’:

  intersect, setdiff, setequal, union

Using Row.names as id variables
mv: cannot stat 'trimmed_accepted': No such file or directory

Work dir:
/mnt/scratch/Sequencing/kk/miRNA/work/7a/0a83a1a8143700ff2cb89b48842ced

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

Hi,
The error is " Error executing process > 'BARPLOTS' "when doing a group comparison analysis with 3 controls and 3 cases.
.command.err file contents :
Warning message:
replacing previous import ‘vctrs::data_frame’ by ‘tibble::data_frame’ when loading ‘dplyr’
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 7301 did not have 7 elements
Calls: read.table -> scan
Execution halted

The last row has only 5 columns, seems like raw counts for 2 files are missing?

Thank you

If you see the error here:

CAPSULE EXCEPTION: java.io.IOException: Cannot run program "/usr/bin/java/bin/java": error=20, Not a directory (for stack trace, run with -Dcapsule.log=verbose)
Unable to initialize nextflow environment

Please unset your JAVA_HOME:
unset JAVA_HOME

Hi,

Hope you are doing well.

I noticed that for one of my datasets the combined score was 0 for all features when doing a group comparison. On further investigation, I found that there were significant results returned by the Fisher's method. When I went debugging I found that the p-value for one of the gene was almost 0 and in CombinedScore.R when obtaining -log10 this was returning infinity. I found a check for infinity for the DeSeq2 method in the same file so I have put the same check for Fisher's method to resolve this.

Thank you,
Sharada

When starting the example analysis for a single file or a multi file analysis without layout then nextflow throws the error
"Cannot invoke method startsWith() on null object". While it is working fine using the group comparison adding the layout option.

Hello,
I had lots of erros while installing. I tried to install manually. How can I solve these? conda env create -f tsRNAsearch/environment.yml is stuck at solving environment phase.

(base) conda env create -f environment.yml
Collecting package metadata (repodata.json): done
Solving environment: \

Here are working, step1:

conda create -y -n tsrnasearch_env python=2.7.15 r=3.5.1
conda activate tsrnasearch_env
conda install -y curl=7.64.0
conda install -y -c bioconda cutadapt=1.18
conda install -y -c bioconda fastqc=0.11.9
conda install -y -c conda-forge ghostscript=9.22
conda install -y -c conda-forge libgit2=0.27.8
conda install -y numpy=1.15.4
conda install -y openssl=1.0.2u
conda install -y pandoc=2.10
conda install -y pip=20.1.1
conda install -y pigz=2.3.4
conda install -y python=2.7.15
conda install -y -c r r=3.5.1
conda install -y -c r r-boot=1.3_20
conda install -y -c r r-checkpoint=0.4.4
conda install -y -c r r-class=7.3_14
conda install -y -c r r-cluster=2.0.7_1
conda install -y -c r r-codetools=0.2_15
conda install -y -c r r-curl=3.2
conda install -y -c r r-deployrrserve=9.0.0
conda install -y -c r r-doparallel=1.0.13
conda install -y -c r r-foreach=1.5.0
conda install -y -c r r-foreign=0.8_70
conda install -y -c r r-iterators=1.0.10
conda install -y -c r r-jsonlite=1.5
conda install -y -c r r-kernsmooth=2.23_15
conda install -y -c r r-lattice=0.20_35
conda install -y -c r r-mass=7.3_49
conda install -y -c r r-matrix=1.2_14
conda install -y -c r r-mgcv=1.8_23
conda install -y -c r r-microsoftr=3.5.0.108
conda install -y -c r r-nlme=3.1_137
conda install -y -c r r-nnet=7.3_12
conda install -y -c r r-png=0.1_7
conda install -y -c r r-r6=2.2.2
conda install -y -c r r-recommended=3.5.1
conda install -y -c r r-revoioq=10.0.0
conda install -y -c r r-revomods=11.0.0
conda install -y -c r r-revoutils=11.0.0
conda install -y -c r r-revoutilsmath=11.0.0
conda install -y -c r r-rpart=4.1_13
conda install -y -c r r-runit=0.4.26
conda install -y -c r r-spatial=7.3_11
conda install -y -c r r-survival=2.41_3
conda install -y -c r samtools=1.9
conda install -y -c r star=2.5.2b
conda install -y -c r subread=2.0.1=hed695b0_0
conda install -y -c r trim-galore=0.4.1
pip install multiqc==0.4
conda install -c bioconda nextflow

Here are not working, step2: Rscript bin/InstallPackages.R

Rscript bin/InstallPackages_GeneralVersions.R
Loading required package: BiocManager
Loading required package: git2r
Loading required package: ggplot2
Loading required package: ggrepel
Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
Loading required package: EnhancedVolcano
[1] "Installing EnhancedVolcano..."
Bioconductor version 3.8 (BiocManager 1.30.1), R 3.5.1 (2018-07-02)
Installing package(s) 'BiocVersion', 'EnhancedVolcano'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/workflows/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Error in library(EnhancedVolcano) :
  there is no package called ‘EnhancedVolcano’
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘EnhancedVolcano’
2: packages ‘BiocVersion’, ‘EnhancedVolcano’ are not available (for R version 3.5.1)
Execution halted

Alternatively:

Rscript bin/InstallPackages.R
Loading required package: BiocManager
Loading required package: devtools

Attaching package: ‘devtools’

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

    install

Loading required package: git2r
Loading required package: ggplot2
Loading required package: ggrepel
Loading required package: VennDiagram
Loading required package: grid
Loading required package: futile.logger
Loading required package: EnhancedVolcano
[1] "Installing EnhancedVolcano..."
Bioconductor version 3.8 (BiocManager 1.30.1), R 3.5.1 (2018-07-02)
Installing package(s) 'BiocVersion', 'EnhancedVolcano'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/workflows/src/contrib:
  Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Error in library(EnhancedVolcano) :
  there is no package called ‘EnhancedVolcano’
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘EnhancedVolcano’
2: packages ‘BiocVersion’, ‘EnhancedVolcano’ are not available (for R version 3.5.1)
Execution halted

Hi,

This issue occurs only in group comparison analysis.
I have 3 files for control and 3 files for treatment which I’m running a group comparison analysis on. The SAMcollapse.py file (called in BAM_COLLAPSE module) does not return any matches for one of the files(counterGroup in the results for this file is 0), this results in the values being set to NA in Combined_case_tRNAs-almost-mapped_RPM.depth and throws an error in the DATA_TRANSFORMATIONS module when calculating mean(of the column with NA). Is it possible to handle the absence tRNAgroups in a file without throwing an error?

Thank you

Hello,
After a successful install and testing, the command gives this repo error.

nextflow run tsRNAsearch --species human --input_dir /fastq --output_dir /tsRNAsearch --layout tsRNAsearch_layout.csv

The error:

N E X T F L O W  ~  version 19.01.0
Pulling nextflow-io/tsRNAsearch ...
Cannot find `nextflow-io/tsRNAsearch` -- Make sure exists a GitHub repository at this address `https://github.com/nextflow-io/tsRNAsearch`

Here nextflow info:

nextflow info
  Version: 19.01.0 build 5050
  Modified: 22-01-2019 11:19 UTC (14:19 EEST)
  System: Linux 3.10.0-1062.4.1.el7.x86_64
  Runtime: Groovy 2.5.5 on OpenJDK 64-Bit Server VM 10.0.2+13
  Encoding: UTF-8 (UTF-8)

What should I check? Could anyone help?

Hey,

I recently noticed a Bug in the software. Whenever you specify your file for the group comparsion (layout file). It seems that the sample names are automatically sorted so that the group annotation for each file is not considered and therefore the group name not assigned accordingly.

As an example if I've samples called

1901_0001.fq.gz, ctrl
1905_0001.fq.gz, ctrl
1902_0001.fq.gz, ko
1903_0001.fq.gz, ko

the 1902 and the 1901 sample are considered as ctrl sample and the 03,05 sample as ko sample for the group analysis while the layout annotation file is neglected. Hope this helps to improve the situation.

Otherwise nice tool!