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Home Page: https://nf-co.re/rnasplice
License: MIT License
rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
Home Page: https://nf-co.re/rnasplice
License: MIT License
Dear All,
As anticipated here, #71, I am now facing an issue with run_stager command. Here are relevant info. Many thks
run_stager.R CP-Brain DEXSeqResults.CP-Brain.tsv perGeneQValue.CP-Brain.tsv dexseq
nextflow run nf-core/rnasplice --input $wd/samplesheet.csv \
--contrasts $wd/contrast.csv \
--outdir splice_attempt1 \
--genome GRCm38 \
--aligner star \
--min_samps_gene_expr 2 \
--min_samps_feature_expr 2 \
--min_gene_expr 5 \
--min_feature_expr 5 \
--min_feature_prop 0.2 \
--dexseq_exon true \
--edger_exon true\
--rmats true \
--rmats_read_len 75 \
--save_reference true \
--sashimi_plot true \
-config config.config \
-profile docker \
-r dev
exit 0
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:STAGER (1)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:STAGER (1)` terminated with an error exit status (1)
Command executed:
run_stager.R CP-Brain DEXSeqResults.CP-Brain.tsv perGeneQValue.CP-Brain.tsv dexseq
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:STAGER":
r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
bioconductor-stager: $(Rscript -e "library(stageR); cat(as.character(packageVersion('stageR')))")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'stageR'
The following object is masked from 'package:methods':
getMethod
Error in `[<-`(`*tmp*`, idCon, 1, value = unlist(txLevelAdjustments)) :
subscript out of bounds
Calls: stageWiseAdjustment -> stageWiseAdjustment -> .local -> .stageWiseTest
Execution halted
[nextflow.log](https://github.com/nf-core/rnasplice
splicing_P107513878.log
/files/12173874/nextflow.log)
nextflow/23.04.1
debian 10
slurm
dev version
Not a bug as such, but more of a missing argument which is critical for rMATS.
one of the key rMATS arguments is libType
(https://github.com/Xinglab/rmats-turbo?tab=readme-ov-file#all-arguments):
--libType {fr-unstranded,fr-firststrand,fr-secondstrand}
Library type. Use fr-firststrand or fr-secondstrand
for strand-specific data. Only relevant to the prep
step, not the post step. Default: fr-unstranded
however in the rnasplice docs I don't see it exposed in the pipeline. Is is possible to choose the library type and I just missed?
No response
No response
No response
Dear All, I am testing the pipeline and I am facing the following error,
Not all conditions are included in the contrast file.
Thanks for your support
Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)` terminated with an error exit status (1)
Command executed:
run_drimseq_filter.R salmon.merged.txi.dtu.rds q.tx2gene.tsv samplesheet.csv \
4 \
2 \
2 \
10 \
0.1 \
10
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER":
r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
bioconductor-drimseq: $(Rscript -e "library(DRIMSeq); cat(as.character(packageVersion('DRIMSeq')))")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
Attaching package: 'DRIMSeq'
The following object is masked from 'package:base':
proportions
Error in .local(x, ...) :
min_samps_gene_expr >= 0 && min_samps_gene_expr <= ncol(x@counts) is not TRUE
Calls: <Anonymous> -> <Anonymous> -> .local -> stopifnot
Execution halted
nextflow run nf-core/rnasplice --input $wd/samplesheet.csv \
--contrasts $wd/contrast.csv \
--outdir test \
--genome GRCm38 \
-profile singularity \
--aligner star \
--dexseq_exon \
--edger_exon \
--rmats \
--rmats_read_len 75 \
--save_reference true \
--sashimi_plot true \
-config config.config \
-r dev
nextflow/22.10.4
HPC - slurm
Operating System: Debian GNU/Linux 10 (buster)
When using the process$scratch
variable in the configuration file, NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI fails by looking in the scratch directory instead of where the pickle files actually are. Here, process$scratch
is set to $TMPDIR
, which gets expanded to /local/xxxxx/20738687/cluster_tmp
.
However, then MISO fails with:
Exception: Error: no filename /local/xxxxx/20738687/cluster_tmp/nxf.R4ElqFeq2j/index/chrX/ENSG00000004961.pickle
The pickle files are however actually in the output directory, not the scratch directory:
(base) -bash-4.2$ find test2 -name *.pickle | head
test2/misopy/index/chrX/ENSG00000130962.pickle
test2/misopy/index/chrX/ENSG00000126952.pickle
test2/misopy/index/chrX/ENSG00000242013.pickle
test2/misopy/index/chrX/ENSG00000196632.pickle
test2/misopy/index/chrX/ENSG00000130830.pickle
test2/misopy/index/chrX/ENSG00000184033.pickle
test2/misopy/index/chrX/ENSG00000101892.pickle
test2/misopy/index/chrX/ENSG00000133149.pickle
test2/misopy/index/chrX/ENSG00000165194.pickle
test2/misopy/index/chrX/ENSG00000198689.pickle
Full error:
-[nf-core/rnasplice] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (1)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (1)` terminated with an error exit status (1)
Command executed:
sashimi_plot --plot-event ENSG00000004961 index miso_settings.txt --output-dir sashimi
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI":
python: $(python --version | sed "s/Python //g")
misopy: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('misopy').version)")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_TMPDIR as environment variable will not be supported in the future, use APPTAINERENV_TMPDIR instead
WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_NXF_DEBUG as environment variable will not be supported in the future, use APPTAINERENV_NXF_DEBUG instead
/usr/local/lib/python2.7/site-packages/matplotlib/cbook/deprecation.py:107: MatplotlibDeprecationWarning: The mpl_toolkits.axes_grid module was deprecated in version 2.1. Use mpl_toolkits.axes_grid1 and mpl_toolkits.axisartist provies the same functionality instead.
warnings.warn(message, mplDeprecation, stacklevel=1)
Traceback (most recent call last):
File "/usr/local/bin/sashimi_plot", line 11, in <module>
sys.exit(main())
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/sashimi_plot.py", line 276, in main
plot_label=plot_label)
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/sashimi_plot.py", line 153, in plot_event
plot_label=plot_label)
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/plot_utils/plot_gene.py", line 675, in plot_density_from_file
parseGene(pickle_filename, event)
File "/usr/local/lib/python2.7/site-packages/misopy/parse_gene.py", line 11, in parseGene
raise Exception, "Error: no filename %s" %(pickle_filename)
Exception: Error: no filename /local/xxxxx/20738687/cluster_tmp/nxf.R4ElqFeq2j/index/chrX/ENSG00000004961.pickle
nextflow run nf-core/rnasplice -profile test -c dkfz.config --outdir test2 -r dev
params {
config_profile_description = 'Deutsches Krebsforschungszentrum (DKFZ) HPC cluster profile provided by nf-core/configs'
config_profile_contact = 'Kübra Narcı [email protected]'
config_profile_name = 'DKFZ cluster'
max_cpus = 30
max_memory = '250.GB'
max_time = '48.h'
}
singularity {
enabled = true
autoMounts = true
}
process {
executor = 'lsf'
clusterOptions = '-L /bin/bash'
scratch = '$TMPDIR'
}
executor {
name = 'lsf'
perTaskReserve = false
perJobMemLimit = true
queueSize = 10
submitRateLimit = '3 sec'
}
Hi, I passed the test samples. But when I run on my samples (BAM+rMats). I got empty rMats output. There was no error reported, showing completed.
$ nextflow run software/rnasplice -profile docker --input nf_samplesheet.csv --contrasts nf_contrastsheet.csv --genome GRCh38 --outdir myenv
nextflow.log
nextflow.config.log
No response
Event ENSG00000005302 not found in pickled directory index. Are you sure this is the right directory for the event?
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (2)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (2)` terminated with an error exit status (1)
Command executed:
sashimi_plot --plot-event ENSG00000005302 index miso_settings.txt --output-dir sashimi
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI":
python: $(python --version | sed "s/Python //g")
misopy: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('misopy').version)")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
/usr/local/lib/python2.7/site-packages/matplotlib/cbook/deprecation.py:107: MatplotlibDeprecationWarning: The mpl_toolkits.axes_grid module was deprecated in version 2.1. Use mpl_toolkits.axes_grid1 and mpl_toolkits.axisartist provies the same functionality instead.
warnings.warn(message, mplDeprecation, stacklevel=1)
Traceback (most recent call last):
File "/usr/local/bin/sashimi_plot", line 11, in <module>
sys.exit(main())
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/sashimi_plot.py", line 276, in main
plot_label=plot_label)
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/sashimi_plot.py", line 142, in plot_event
%(event_name, pickle_dir)
Exception: Event ENSG00000005302 not found in pickled directory index. Are you sure this is the right directory for the event?
Work dir:
/flash/SciTechGrp/Zain/54/4ab0250756d10788d62592d4524e58
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
No response
No response
Basically what the title says. When running the pipeline with --gencode
, the default value for --miso_genes
should be "ENSG00000004961.15, ENSG00000005302.19, ENSG00000147403.18"
, otherwise the pipeline will fail to run properly.
More info can be found here: #72 (comment)
No response
No response
No response
I have a question regarding a parameter in the stager screening procedure:
/bin/run_stager.R
line 147:
object <- stageRTx(
pScreen = output[["pScreen"]],
pConfirmation = output[["pConfirmation"]],
tx2gene = output[["tx2gene"]],
pScreenAdjusted = FALSE
)
Why is pScreenAdjusted set to FALSE, I thought that the perGeneQvalue outputed by DEXseq is already adjusted, as described by the function helper in DEXSeq, which would mean the parameter should be set to TRUE here. This is also set to TRUE in the original workflow proposed in:
https://f1000research.com/articles/7-952/v3
Motivation
Many projects will use a combination of differentialabundance
and rnasplice
analysis, using as input the processed data from rnaseq
. Thus keeping the workflows as consistent as possible would facilitate reusing files, for the user, and code, for developers.
Suggestion
The column names in the contrasts file are different from those of the differentialabundance
pipeline. Would it possible to uniformize them?
in this pipeline contrast,treatment,control
would becomes id,reference,target
as in differentialabundance This would allow the re-use of the contrast file across the two nf-core pipelines for at least the simplest comparisons.
I am suggesting the change here because it seems to me that that differentialabundance is the more mature of the two and thus change there would result in more things breaking.
MISO_INDEX runs and appears to create an output file "/index/genes.gff" (according to command.log), but the pipeline breaks with the below error.
Upon checking the work directory, there is only the log files; no ".gff".
nextflow -c nextflow.config run nf-core/rnasplice -r dev -
profile test --outdir 's3://mdibl-jhfuqua/'
Aug-22 14:15:28.171 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RNASPLIC
E:RNASPLICE:VISUALISE_MISO:MISO_INDEX'
Caused by:
Missing output file(s) `index` expected by process `NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_INDEX`
Command executed:
index_gff --index genes_chrX_genes.gff3 index
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_INDEX":
python: $(python --version | sed "s/Python //g")
misopy: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('misopy').version)")
END_VERSIONS
Command exit status:
0
Command output:
(empty)
No response
I am trying to apply RNA splicing pipeline for DEU approach. However, I get this error which refers to some DTU approach, which I don't want to do so far (I will do it later).
Therefore, I don't understand what the pipeline is trying to do or how I could solve it.
Thank you.
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DEXSEQ_DTU (1)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DEXSEQ_DTU (1)` terminated with an error exit status (1)
Command executed:
run_dexseq_dtu.R samples.tsv Contrast_sheet_rnasplice.csv counts.tsv 10
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DEXSEQ_DTU":
r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
bioconductor-dexseq: $(Rscript -e "library(DEXSeq); cat(as.character(packageVersion('DEXSeq')))")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
anyMissing, rowMedians
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
The following object is masked from 'package:Biobase':
rowMedians
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: DESeq2
Loading required package: AnnotationDbi
Loading required package: RColorBrewer
converting counts to integer mode
Warning message:
In DESeqDataSet(rse, design, ignoreRank = TRUE) :
some variables in design formula are characters, converting to factors
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA) :
replacement has 1 row, data has 0
Calls: mapply ... colData<- -> makeBigModelFrame -> $<- -> $<-.data.frame
Execution halted
No response
No response
I believe this could be a bug as I can't see any reason as far as I know for why this is not working.
The error is related to the contrast file (below attached). I also attached the samplesheet. csv
nextflow run nf-core/rnasplice -r 1.0.1 -name NUTRIPROG1 -profile singularity -params-file nf-
params.json
{
"input": ".\/samples\/samplesheet.csv",
"contrasts": ".\/samples\/contrast.csv",
"outdir": "\/uoa\/home\/r01mt19\/sharedscratch\/NUTRIPROG\/NUTRIPROG1_splice\/results",
"email": "[email protected]",
"multiqc_title": "NP1_MultiQC",
"fasta": ".\/genome\/Salmo_salar.Ssal_v3.1.dna.toplevel.fa",
"gtf": ".\/genome\/Salmo_salar.Ssal_v3.1.109.gtf",
"aligner": "star_salmon",
"rmats": true,
"rmats_read_len": 2322889764,
"dexseq_exon": true,
"edger_exon": true,
"dexseq_dtu": true
}
Jan-02 07:03:34.840 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-02 07:03:34.841 [Task submitter] INFO nextflow.Session - [d9/23184d] Submitted process > NFCORE_RNASPLICE:RNASPLICE:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)
Jan-02 07:03:37.472 [Actor Thread 45] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0 path=/uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/singularity/depot.galaxyproject.org-singularity-gffread-0.12.1--h8b12597_0.img
Jan-02 07:03:37.497 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-02 07:03:37.498 [Task submitter] INFO nextflow.Session - [d3/ed09de] Submitted process > NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_SALMON:GFFREAD_TX2GENE (Salmo_salar.Ssal_v3.1.109.gtf)
Jan-02 07:03:37.524 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-02 07:03:37.525 [Task submitter] INFO nextflow.Session - [85/777fd2] Submitted process > NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_STAR_SALMON:GFFREAD_TX2GENE (Salmo_salar.Ssal_v3.1.109.gtf)
Jan-02 07:03:38.495 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NFCORE_RNASPLICE:RNASPLICE:CONTRASTS_CHECK:CONTRASTSHEET_CHECK (contrast.csv); status: COMPLETED; exit: 1; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/b3/1d2619589f656c58da4128c4fee2c6]
Jan-02 07:03:38.502 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_RNASPLICE:RNASPLICE:CONTRASTS_CHECK:CONTRASTSHEET_CHECK (contrast.csv); work-dir=/uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/b3/1d2619589f656c58da4128c4fee2c6
error [nextflow.exception.ProcessFailedException]: Process NFCORE_RNASPLICE:RNASPLICE:CONTRASTS_CHECK:CONTRASTSHEET_CHECK (contrast.csv)
terminated with an error exit status (1)
Jan-02 07:03:38.527 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:CONTRASTS_CHECK:CONTRASTSHEET_CHECK (contrast.csv)'
Caused by:
Process NFCORE_RNASPLICE:RNASPLICE:CONTRASTS_CHECK:CONTRASTSHEET_CHECK (contrast.csv)
terminated with an error exit status (1)
Command executed:
check_contrastsheet.py contrast.csv contrastsheet.valid.csv
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:CONTRASTS_CHECK:CONTRASTSHEET_CHECK":
python: $(python --version | sed 's/Python //g')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
[CRITICAL] The contrast sheet must contain these column headers: control, treatment, contrast.
Work dir:
/uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/b3/1d2619589f656c58da4128c4fee2c6
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
Jan-02 07:03:38.548 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Jan-02 07:03:38.558 [main] DEBUG nextflow.Session - Session await > all processes finished
Jan-02 07:03:38.598 [Actor Thread 59] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; work-dir=null
error [java.lang.InterruptedException]: java.lang.InterruptedException
Jan-02 07:03:38.598 [Actor Thread 52] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI; work-dir=null
error [java.lang.InterruptedException]: java.lang.InterruptedException
Jan-02 07:03:38.598 [Actor Thread 54] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE; work-dir=null
error [java.lang.InterruptedException]: java.lang.InterruptedException
Jan-02 07:03:38.599 [Actor Thread 66] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION; work-dir=null
error [java.lang.InterruptedException]: java.lang.InterruptedException
Jan-02 07:03:38.599 [Actor Thread 57] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE; work-dir=null
error [java.lang.InterruptedException]: java.lang.InterruptedException
Jan-02 07:03:38.599 [Actor Thread 73] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI; work-dir=null
error [java.lang.InterruptedException]: java.lang.InterruptedException
Jan-02 07:03:38.599 [Actor Thread 15] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jan-02 07:03:38.622 [Actor Thread 46] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jan-02 07:03:38.622 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: NFCORE_RNASPLICE:RNASPLICE:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv); status: COMPLETED; exit: 0; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/d9/23184d89571da1adf0b9d1b84fead3]
Jan-02 07:03:38.660 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=240; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jan-02 07:03:49.495 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:SUBREAD_FLATTENGTF (Salmo_salar.Ssal_v3.1.109.gtf); status: COMPLETED; exit: 0; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/ca/b218a21cf5ad63f3b7a2ebe21baa16]
Jan-02 07:03:50.848 [Actor Thread 60] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/gffread:0.12.7--hdcf5f25_3 path=/uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/singularity/depot.galaxyproject.org-singularity-gffread-0.12.7--hdcf5f25_3.img
Jan-02 07:03:53.447 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: COMPLETED; exit: 0; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/f3/f45ec57c6bbf46ee01975e391ba395]
Jan-02 07:03:53.586 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:CUSTOM_GETCHROMSIZES > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
Jan-02 07:04:12.536 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_STAR_SALMON:GFFREAD_TX2GENE (Salmo_salar.Ssal_v3.1.109.gtf); status: COMPLETED; exit: 0; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/85/777fd276623cca8d8517dd5778361b]
Jan-02 07:04:17.214 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_SALMON:GFFREAD_TX2GENE (Salmo_salar.Ssal_v3.1.109.gtf); status: COMPLETED; exit: 0; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/d3/ed09dedac6f08923075716649cb2a3]
Jan-02 07:07:49.055 [Actor Thread 49] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/htseq:2.0.2--py310ha14a713_0 path=/uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/singularity/depot.galaxyproject.org-singularity-htseq-2.0.2--py310ha14a713_0.img
Jan-02 07:07:50.535 [Actor Thread 68] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /uoa/home/r01mt19/.nextflow/assets/nf-core/rnasplice/bin/dexseq_prepare_annotation.py
Jan-02 07:08:10.323 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:GTF_GENE_FILTER (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: COMPLETED; exit: 0; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/25/fd64ccb527636c0b5a95a48cb29b50]
Jan-02 07:08:30.524 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 07:08:51.849 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 2 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
Jan-02 07:13:30.544 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 07:13:51.924 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 2 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
Jan-02 07:18:30.558 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 07:18:52.161 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 2 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
Jan-02 07:19:16.853 [Actor Thread 44] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/suppa:2.3--py36_0 path=/uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/singularity/depot.galaxyproject.org-singularity-suppa-2.3--py36_0.img
Jan-02 07:23:30.602 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 07:23:52.995 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
~> TaskHandler[id: 10; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/bf/41a0a46836f39bde096dc6392f5e27]
~> TaskHandler[id: 14; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/8d/f48e42145f5a63728ea2a7a6bb2f3d]
~> TaskHandler[id: 13; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/2a/100525ac82b2d516aacb8fc9b3a1c0]
~> TaskHandler[id: 11; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/84/134b660a04bcd3c2e75f3e7e725a1e]
Jan-02 07:28:30.642 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 07:28:53.907 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
~> TaskHandler[id: 10; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/bf/41a0a46836f39bde096dc6392f5e27]
~> TaskHandler[id: 14; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/8d/f48e42145f5a63728ea2a7a6bb2f3d]
~> TaskHandler[id: 13; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/2a/100525ac82b2d516aacb8fc9b3a1c0]
~> TaskHandler[id: 11; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/84/134b660a04bcd3c2e75f3e7e725a1e]
Jan-02 07:33:30.714 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 07:33:54.088 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
~> TaskHandler[id: 10; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/bf/41a0a46836f39bde096dc6392f5e27]
~> TaskHandler[id: 14; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/8d/f48e42145f5a63728ea2a7a6bb2f3d]
~> TaskHandler[id: 13; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/2a/100525ac82b2d516aacb8fc9b3a1c0]
~> TaskHandler[id: 11; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/84/134b660a04bcd3c2e75f3e7e725a1e]
Jan-02 07:38:30.742 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 07:38:54.867 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
~> TaskHandler[id: 10; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/bf/41a0a46836f39bde096dc6392f5e27]
~> TaskHandler[id: 14; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/8d/f48e42145f5a63728ea2a7a6bb2f3d]
~> TaskHandler[id: 13; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/2a/100525ac82b2d516aacb8fc9b3a1c0]
~> TaskHandler[id: 11; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/84/134b660a04bcd3c2e75f3e7e725a1e]
Jan-02 07:43:30.760 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 07:43:54.988 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
~> TaskHandler[id: 10; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/bf/41a0a46836f39bde096dc6392f5e27]
~> TaskHandler[id: 14; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/8d/f48e42145f5a63728ea2a7a6bb2f3d]
~> TaskHandler[id: 13; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/2a/100525ac82b2d516aacb8fc9b3a1c0]
~> TaskHandler[id: 11; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/84/134b660a04bcd3c2e75f3e7e725a1e]
Jan-02 07:48:30.764 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 07:48:55.235 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
~> TaskHandler[id: 10; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/bf/41a0a46836f39bde096dc6392f5e27]
~> TaskHandler[id: 14; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/8d/f48e42145f5a63728ea2a7a6bb2f3d]
~> TaskHandler[id: 13; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/2a/100525ac82b2d516aacb8fc9b3a1c0]
~> TaskHandler[id: 11; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/84/134b660a04bcd3c2e75f3e7e725a1e]
Jan-02 07:53:30.785 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 07:53:55.632 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
~> TaskHandler[id: 10; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/bf/41a0a46836f39bde096dc6392f5e27]
~> TaskHandler[id: 14; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/8d/f48e42145f5a63728ea2a7a6bb2f3d]
~> TaskHandler[id: 13; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/2a/100525ac82b2d516aacb8fc9b3a1c0]
~> TaskHandler[id: 11; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/84/134b660a04bcd3c2e75f3e7e725a1e]
Jan-02 07:58:30.875 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 07:58:56.483 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
~> TaskHandler[id: 10; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/bf/41a0a46836f39bde096dc6392f5e27]
~> TaskHandler[id: 14; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/8d/f48e42145f5a63728ea2a7a6bb2f3d]
~> TaskHandler[id: 13; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/2a/100525ac82b2d516aacb8fc9b3a1c0]
~> TaskHandler[id: 11; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/84/134b660a04bcd3c2e75f3e7e725a1e]
Jan-02 08:03:30.920 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 08:03:57.280 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
~> TaskHandler[id: 10; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/bf/41a0a46836f39bde096dc6392f5e27]
~> TaskHandler[id: 14; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/8d/f48e42145f5a63728ea2a7a6bb2f3d]
~> TaskHandler[id: 13; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/2a/100525ac82b2d516aacb8fc9b3a1c0]
~> TaskHandler[id: 11; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/84/134b660a04bcd3c2e75f3e7e725a1e]
Jan-02 08:08:30.937 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 08:08:57.344 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
~> TaskHandler[id: 10; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/bf/41a0a46836f39bde096dc6392f5e27]
~> TaskHandler[id: 14; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/8d/f48e42145f5a63728ea2a7a6bb2f3d]
~> TaskHandler[id: 13; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/2a/100525ac82b2d516aacb8fc9b3a1c0]
~> TaskHandler[id: 11; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/84/134b660a04bcd3c2e75f3e7e725a1e]
Jan-02 08:13:30.986 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 08:13:57.957 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
~> TaskHandler[id: 10; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/bf/41a0a46836f39bde096dc6392f5e27]
~> TaskHandler[id: 14; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/8d/f48e42145f5a63728ea2a7a6bb2f3d]
~> TaskHandler[id: 13; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/2a/100525ac82b2d516aacb8fc9b3a1c0]
~> TaskHandler[id: 11; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/84/134b660a04bcd3c2e75f3e7e725a1e]
Jan-02 08:18:31.027 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 08:18:58.269 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
~> TaskHandler[id: 10; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/bf/41a0a46836f39bde096dc6392f5e27]
~> TaskHandler[id: 14; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/8d/f48e42145f5a63728ea2a7a6bb2f3d]
~> TaskHandler[id: 13; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/2a/100525ac82b2d516aacb8fc9b3a1c0]
~> TaskHandler[id: 11; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/84/134b660a04bcd3c2e75f3e7e725a1e]
Jan-02 08:23:31.086 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 08:23:59.155 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
~> TaskHandler[id: 10; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/bf/41a0a46836f39bde096dc6392f5e27]
~> TaskHandler[id: 14; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/8d/f48e42145f5a63728ea2a7a6bb2f3d]
~> TaskHandler[id: 13; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/2a/100525ac82b2d516aacb8fc9b3a1c0]
~> TaskHandler[id: 11; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/84/134b660a04bcd3c2e75f3e7e725a1e]
Jan-02 08:28:31.088 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: RUNNING; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 08:28:44.984 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:STAR_GENOMEGENERATE (Salmo_salar.Ssal_v3.1.dna.toplevel.fa); status: COMPLETED; exit: 0; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/91/54dc6a038f8be4c73d798b925c52d6]
Jan-02 08:28:46.453 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Jan-02 08:28:46.656 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jan-02 08:28:46.816 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Jan-02 08:28:50.996 [main] INFO nextflow.Nextflow - -�[0;35m[nf-core/rnasplice]�[0;32m Sent summary e-mail to [email protected] (sendmail)-
Jan-02 08:28:52.105 [main] INFO nextflow.Nextflow - -�[0;35m[nf-core/rnasplice]�[0;31m Pipeline completed with errors�[0m-
Jan-02 08:28:56.672 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=7; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=6; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=17h 6m 32s; failedDuration=3.6s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=8; peakCpus=21; peakMemory=114 GB; ]
Jan-02 08:28:56.673 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jan-02 08:28:56.715 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jan-02 08:28:59.488 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 6 -- tasks to be submitted are shown below
~> TaskHandler[id: 8; name: NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3; status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/1a/89621de8f0a100a313ae6c641a01c5]
~> TaskHandler[id: 7; name: NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/6c/c1922f429ef61c8742847108caf556]
~> TaskHandler[id: 10; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/bf/41a0a46836f39bde096dc6392f5e27]
~> TaskHandler[id: 14; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/8d/f48e42145f5a63728ea2a7a6bb2f3d]
~> TaskHandler[id: 13; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/2a/100525ac82b2d516aacb8fc9b3a1c0]
~> TaskHandler[id: 11; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (Salmo_salar.Ssal_v3.1.109.gtf); status: NEW; exit: -; error: -; workDir: /uoa/scratch/users/r01mt19/NUTRIPROG/NUTRIPROG1_splice/work/84/134b660a04bcd3c2e75f3e7e725a1e]
Jan-02 08:29:15.669 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jan-02 08:29:18.993 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jan-02 08:29:18.994 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin '[email protected]'
Jan-02 08:29:18.995 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation
Jan-02 08:29:19.249 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Jan-02 08:29:19.501 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
HPC - slurm - singularity
nextflow/23.10.0
nf-core/rnasplice -r 1.0.1
Opening a new report as requested by @jma1991
The issue is described here and in subsequent messages: #85 (comment)
The command and input files are listed in the first message here: #85
No response
No response
No response
I am constantly getting this error. It is already mentioned in other issues, but I was not able to fix it. Any help will be appreciated. Thanks. "
The exit status of the task that caused the workflow execution to fail was: 1
Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (2)'
Caused by:
Process NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (2)
terminated with an error exit status (1)
Command executed:
sashimi_plot --plot-event ENSG00000005302.19 index miso_settings.txt --output-dir sashimi
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI":
python: $(python --version | sed "s/Python //g")
misopy: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('misopy').version)")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
/usr/local/lib/python2.7/site-packages/matplotlib/cbook/deprecation.py:107: MatplotlibDeprecationWarning: The mpl_toolkits.axes_grid module was deprecated in version 2.1. Use mpl_toolkits.axes_grid1 and mpl_toolkits.axisartist provies the same functionality instead.
warnings.warn(message, mplDeprecation, stacklevel=1)
Traceback (most recent call last):
File "/usr/local/bin/sashimi_plot", line 11, in
sys.exit(main())
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/sashimi_plot.py", line 276, in main
plot_label=plot_label)
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/sashimi_plot.py", line 142, in plot_event
%(event_name, pickle_dir)
Exception: Event ENSG00000005302.19 not found in pickled directory index. Are you sure this is the right directory for the event?
Work dir:
/home/hamalibt/Splicesome_Project/RNA_SEQ_ARGLU1KO_VS_MCF7WT/work/6a/df958b424331c70ec5aaa5eeb10caf
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
"
nextflow run nf-core/rnasplice \
-profile singularity \
--input /path/to/samplesheet.csv \
--contrasts /path/to/contrastsheet.csv \
--outdir /path/to/output_directory \
--genome GRCh38 \
--aligner star_salmon \
--save_reference \
--dexseq_dtu \
--min_samps_gene_expr 6 \
--min_gene_expr 10 \
--min_samps_feature_expr 3 \
--min_feature_expr 10 \
--min_samps_feature_prop 3 \
--min_feature_prop 0.1
N E X T F L O W ~ version 23.10.1, local, Apptainer
Hello,
We are attempting to run this pipeline with a rather complex scenario: 850 contrasts and 3400 samples. The processes SPLIT_FILES_TPM
, SPLIT_FILES_IOE
and SPLIT_FILES_IOI
appear to be running very slowly.
For example, looking at SPLIT_FILES_TPM
, this has been running for 12 hours and only produced 61 TPM files so far. At this rate, it should take around 4 weeks to finish this process, before even attempting to run Suppa2...
We have successfully run these samples through nf-core/rnaseq
(which took less than a week on 512 cores and 2 TB of RAM), and nf-core/differentialabundance
(which only took 2 hours to run DESeq2). We now intend to run Suppa2 via this pipeline.
Any advice for speeding things up would be much appreciated. This is the command that we are running:
nextflow run nf-core/rnasplice -r 1.0.2 -c custom.config -params-file params.yml --igenomes_ignore --genome null \
--input /path/to/sample-sheet-rnasplice.csv \
--outdir run-rnasplice -profile docker --source salmon_results \
--fasta /path/to/genome/gencode_v45_spike-ins.fasta \
--gtf /path/to/genome/gencode_v45_spike-ins.gtf \
--star_index /path/to/genome/index/star \
--salmon_index /path/to/genome/index/salmon \
--dexseq_exon false --dexseq_dtu false \
--suppa --suppa_per_local_event \
--contrasts /path/to/contrasts-rnasplice.csv \
--sashimi_plot false
My contrast sheet looks like this:
contrast,treatment,control
KO_CONTROL,KO,CONTROL
then I get
Loading required package: limma
Error in asplit(contrasts, MARGIN = 2) :
dim(x) must have a positive length
however, making a new fake contrast sheet with also the reverse contrast fixes it.
contrast,treatment,control
KO_CONTROL,KO,CONTROL
CONTROL_KO,CONTROL,KO
The exact place the error occurs is in the script run_edger_exon.R
DGELRT.exprs <- mapply(
FUN = glmQLFTest,
contrast = asplit(contrasts, MARGIN = 2),
MoreArgs = list(glmfit = DGEGLM),
SIMPLIFY = FALSE
)
nextflow run \
/omics/groups/xxxxx/internal/xxxxx/src/github.com/dkoppstein/rnasplice \
--input config/samplesheet_splicing.csv \
--contrasts config/contrastsheet_splicing.csv \
--outdir workspace/rnasplice_results_ko_vs_control \
-c config/dkfz.config \
--fasta $(GENOMEDIR)/GRCh38.primary_assembly.genome.fa \
--gtf $(GENOMEDIR)/gencode.v43.annotation.gtf \
--star_index $(GENOMEDIR)/genome/index/star \
--salmon_index $(GENOMEDIR)/genome/index/salmon \
--gencode \
--save_reference \
--min_samps_gene_expr 0 \
--min_samps_feature_expr 0 \
--min_samps_feature_prop 0 \
--min_feature_expr 0 \
--min_feature_prop 0 \
--min_gene_expr 0 \
--miso_genes "ENSG00000004961.15, ENSG00000005302.19, ENSG00000147403.18" \
-resume
touch $@
No response
Nextflow version 23.04.1 build 5866
HPC
lsf executor
Singularity container
CentOS Linux
dev
I'm getting an error message when running rnasplice about the sashimi_plot. The error message is copied below:
-[nf-core/rnasplice] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (3)'
Caused by:
Process NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (3)
terminated with an error exit status (1)
Command executed:
sashimi_plot --plot-event ENSG00000147403 index miso_settings.txt --output-dir sashimi
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI":
python: $(python --version | sed "s/Python //g")
misopy: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('misopy').version)")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
/usr/local/lib/python2.7/site-packages/matplotlib/cbook/deprecation.py:107: MatplotlibDeprecationWarning: The mpl_toolkits.axes_grid module was deprecated in version 2.1. Use mpl_toolkits.axes_grid1 and mpl_toolkits.axisartist provies the same functionality instead.
warnings.warn(message, mplDeprecation, stacklevel=1)
Traceback (most recent call last):
File "/usr/local/bin/sashimi_plot", line 11, in
sys.exit(main())
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/sashimi_plot.py", line 276, in main
plot_label=plot_label)
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/sashimi_plot.py", line 142, in plot_event
%(event_name, pickle_dir)
Exception: Event ENSG00000147403 not found in pickled directory index. Are you sure this is the right directory for the event?
This is the command I ran:
nextflow run nf-core/rnasplice -profile docker -params-file params.yaml
This was my params.yaml file:
input: '/path/samplesheet.csv'
contrasts: '/path/contrastsheet.csv'
outdir: '/path/outdir/'
source: 'fastq'
genome: 'BDGP6'
aligner: 'star_salmon'
save_reference: true
dexseq_dtu: true
min_samps_gene_expr: 6
min_gene_expr: 10
min_samps_feature_expr: 3
min_feature_expr: 10
min_samps_feature_prop: 3
min_feature_prop: 0.1
This was my Contrastsheet:
contrast,treatment,control
AUB_CS,AUB,CS
No response
Nextflow version: version 23.10.0
Linux OS
Version of nf-core/rnasplice 1.0.1
I assume this on your radar, but it looks like gencode
is declared here when it should be params.gencode
?
I'm getting an error with DRIMSeq when I try to run rnasplice. The pipeline works fine with other samples, so I'm not sure what's causing this error.
Command Used:
nextflow run nf-core/rnasplice -profile docker -params-file /path/to/params.yaml
Error message:
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)` terminated with an error exit status (1)
Command executed:
run_drimseq_filter.R salmon.merged.txi.dtu.rds tximport.tx2gene.tsv Arc_RIPseq-samplesheet.csv \
6 \
3 \
3 \
10 \
0.1 \
10
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER":
r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
bioconductor-drimseq: $(Rscript -e "library(DRIMSeq); cat(as.character(packageVersion('DRIMSeq')))")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
Attaching package: 'DRIMSeq'
The following object is masked from 'package:base':
proportions
Error in DRIMSeq::dmDSdata(counts = counts, samples = samps) :
all(samples$sample_id %in% colnames(counts)) is not TRUE
Calls: <Anonymous> -> stopifnot
Execution halted
Samplesheet file:
sample,fastq_1,fastq_2,strandedness,condition
ID11-IP-Arc-R2,/path/to/rawdata/ID11-IP-Arc-R2_1.fastq.gz,/path/to/rawdata/ID11-IP-Arc-R2_2.fastq.gz,unstranded,treatment
IP-Arc-R1,/path/to/rawdata/IP-Arc-R1_1.fastq.gz,/path/to/rawdata/IP-Arc-R1_2.fastq.gz,unstranded,treatment
ID-2-Arc-IP-R3,/path/to/rawdata/ID-2-Arc-IP-R3_1.fastq.gz,/path/to/rawdata/ID-2-Arc-IP-R3_2.fastq.gz,unstranded,treatment
ID-5-Non-IP-R3,/path/to/rawdata/ID-5-Non-IP-R3_1.fastq.gz,/path/to/rawdata/ID-5-Non-IP-R3_2.fastq.gz,unstranded,Control
ID12-Non-Arc-R2,/path/to/rawdata/ID12-Non-Arc-R2_1.fastq.gz,/path/to/rawdata/ID12-Non-Arc-R2_2.fastq.gz,unstranded,Control
Non-Arc-R1,/path/to/rawdata/Non-Arc-R1_1.fastq.gz,/path/to/rawdata/Non-Arc-R1_2.fastq.gz,unstranded,Control
params.yaml file:
input: '/path/to/sequencing_data/Arc_RIPseq-samplesheet.csv'
contrasts: '/path/to/sequencing_data/Arc_RIPseq-contrastsheet.csv'
outdir: '/path/to/sequencing_data/'
fasta: '/home/gimena/reference_files/BDGP6.32_ensemble/Drosophila_melanogaster.BDGP6.32.dna.toplevel.fa'
gtf: '/home/gimena/reference_files/GTF_files/fromEnsembl/Drosophila_melanogaster.BDGP6.32.106.gtf'
source: 'fastq'
aligner: 'star_salmon'
min_samps_gene_expr: 6
min_gene_expr: 10
min_samps_feature_expr: 3
min_feature_expr: 10
min_samps_feature_prop: 3
min_feature_prop: 0.1
sashimi_plot: true
fig_height: 20
fig_width: 20
miso_genes: FBgn0265487
skip_bigwig: false
dexseq_dtu: true
suppa: false
edger_exon: false
dexseq_exon: false
rmats: false
Nextflow Version: version 23.10.0
Linux OS
Version of nf-core/rnasplice 1.0.1
Hello,
I'm getting the error from the title when testing the pipeline, starting from BAM files produced by nf-core/rnaseq. Tested with the latest dev version and Nextflow 23.04.0
. This the the output:
------------------------------------------------------
[- ] process > NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:GUNZIP_GTF -
[- ] process > NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:GTF_GENE_FILTER -
[- ] process > NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA -
[- ] process > NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:CUSTOM_GETCHROMSIZES -
ERROR ~ No such variable: Exception evaluating property 'out' for nextflow.script.ChannelOut, Reason: groovy.lang.MissingPropertyException: No such property: out for class: groovyx.gpars.dataflow.DataflowBroadcast
-- Check script '/data/share/.nextflow/assets/nf-core/rnasplice/./workflows/rnasplice.nf' at line: 175 or see '.nextflow.log' file for more details
The last printed message seems to refer to this part of the code: https://github.com/nf-core/rnasplice/blob/dev/workflows/rnasplice.nf#L175-L179
I am attaching the full log below.
No response
No response
rnasplice/bin/suppa_split_file.R
Line 75 in f70bbce
This error occurred for me when input sample-sheet had sample names with "-" in them.
the workflow ran fine till tximport but below function converted "-" to "." as er default R behaviour
input_file <- read.csv(input_file, sep="\t", header=TRUE)
need to include check.names = F in the read.csv function.
The link from the nf-core pipelines for the rnasplice contrastsheet: https://raw.githubusercontent.com/nf-core/rnasplice/dev/assets/contrastsheet.csv is blank, it looks like it was deleted from the github page under /dev/assets/ could someone re upload the correct contrast sheet, as this is the part of the pipeline I keep getting errors for.
No response
No response
No response
Hi,
I am trying dev version and I encountered the following error:
I have 32 samples total, 4 conditions, 8 samples per condition
Best
Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOE (CP-Cortex)
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOE (CP-Cortex)` terminated with an error exit status (1)
Command executed:
suppa.py \
clusterEvents \
--dpsi CP-Cortex_local_diffsplice.dpsi \
--psivec CP-Cortex_local_diffsplice.psivec \
--dpsi-threshold 0.05 \
--eps 0.05 \
--metric euclidean \
--min-pts 20 \
--groups 1-25,6-27,12-30,17-32 \
--clustering DBSCAN \
-o CP-Cortex_local_cluster
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOE":
suppa: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('suppa').version)")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
ERROR:lib.cluster_tools:Invalid index. Index 32 is larger than the number of columns in the file (16).`
nextflow run nf-core/rnasplice --input $wd/samplesheet.csv \
--contrasts $wd/contrast.csv \
--outdir splice_attempt1 \
--genome GRCm38 \
--aligner star_salmon \
--min_samps_gene_expr 2 \
--min_samps_feature_expr 2 \
--min_gene_expr 5 \
--min_feature_expr 5 \
--min_feature_prop 0.2 \
--dexseq_exon true \
--edger_exon true\
--dexseq_dtu true \
--dtu_txi scaledTPM \
--rmats true \
--rmats_read_len 75 \
--suppa true \
--suppa_per_isoform true \
--save_reference true \
--sashimi_plot true \
-config config.config \
-profile singularity \
-r dev
nextflow/22.10.4
Debian 10
Slurn
Hi,
For one of my contrasts (pdx_41-control_don) the group parameter for CLUSTEREVENTS_IOI (suppa_clusterevents.nf) is assigned incorrectly, so that ERROR:lib.cluster_tools:Invalid index. Index 6 is smaller than the number of columns in the file (7).
occurs. For all other contrasts, the clustergroup assignment works fine.
The related pdx_41-control_don_transcript_diffsplice.psivec file contains seven columns, the correct grouping would be --groups 1-4,5-7
:
transcript_pdx_41_1 transcript_pdx_41_2 transcript_pdx_41_3 transcript_pdx_41_4 transcript_control_don_1 transcript_control_don_2 transcript_control_don_3
ENSG00000290825.1;ENST00000456328.2 1.0 1.0 1.0 1.0 nan nan nan
It seems that the derivation of the clustergroups for this contrast was never started. The related work directory 0d/4f97644516640eda4e35d88e4dab59 is empty.
(base) -bash-4.2$ grep pdx_41-control_don .nextflow.log | grep CLUSTERGROUPS
~> TaskHandler[jobId: null; id: 164; name: NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTERGROUPS_IOI (pdx_41-control_don); status: NEW; exit: -; error: -; workDir: XXX/rnasplice_pdx/work/0d/4f97644516640eda4e35d88e4dab59 started: -; exited: -; ]
activation/XXX/rnasplice_pdx/work/0d/4f97644516640eda4e35d88e4dab59 started: -; exited: -; ]
However, CLUSTEREVENTS_IOI is executed with --groups 1-3,4-6
which causes the error to occur. Could you please help me to understand why and at which point the assignment --groups 1-3,4-6
is made, as CLUSTERGROUPS does not seem to run? Thank you in advance!
Command used:
nextflow run \
$(RNASPLICE_DIR) \
--input config/samplesheet_pdx_group.csv \
--contrasts config/contrastsheet_pdx_group.csv \
--outdir workspace/rnasplice_pdx_group_results \
-c config/XXX.config \
--fasta $(GENOMEDIR)/GRCh38.primary_assembly.genome.fa \
--gtf $(GENOMEDIR)/gencode.v43.annotation.gtf \
--star_index $(GENOMEDIR)/genome/index/star \
--salmon_index $(GENOMEDIR)/genome/index/salmon \
--gencode \
--save_reference \
--save_unaligned \
--min_samps_gene_expr 0 \
--min_samps_feature_expr 0 \
--min_samps_feature_prop 0 \
--min_feature_expr 0 \
--min_feature_prop 0 \
--min_gene_expr 0 \
--miso_genes "ENSG00000211899.10, ENSG00000171862.14, ENSG00000004961.15, ENSG00000005302.19, ENSG00000147403.18"
Output:
-[nf-core/rnasplice] Pipeline completed with errors- [38/1751]
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOI (pdx_41-control_don)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOI (pdx_41-control_don)` terminated with an erro$
exit status (1)
Command executed:
suppa.py \
clusterEvents \
--dpsi pdx_41-control_don_transcript_diffsplice.dpsi \
--psivec pdx_41-control_don_transcript_diffsplice.psivec \
--dpsi-threshold 0.05 \
--eps 0.05 \
--metric euclidean \
--min-pts 20 \
--groups 1-3,4-6 \
--clustering DBSCAN \
-o pdx_41-control_don_transcript_cluster
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:CLUSTEREVENTS_IOI":
suppa: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('suppa').version)")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is prefer
red
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
WARNING: Skipping mount /var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in con
tainer
ERROR:lib.cluster_tools:Invalid index. Index 6 is smaller than the number of columns in the file (7).
Work dir:
XXX/rnasplice_pdx/work/df/888c5d2dcf001bf157d5ddbaffafbb
contrastsheet_pdx_group.csv
samplesheet_pdx_group.csv
CentOS Linux release 7.9.2009 (Core), LSF Cluster
Nextflow version 23.10.1
$(RNASPLICE_DIR) in the pipeline call refers to a fork of nf-core/rnasplice v1.0.2 that increases alignment resources (https://github.com/dkoppstein/rnasplice/tree/increase_sam)
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/rnasplice] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN (ERR204916)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN (ERR204916)` terminated with an error exit status (105)
Command executed:
STAR \
--genomeDir STARIndex \
--readFilesIn input1/ERR204916_1_val_1.fq.gz input2/ERR204916_2_val_2.fq.gz \
--runThreadN 12 \
--outFileNamePrefix ERR204916. \
\
--sjdbGTFfile genes_chrX.gtf \
--outSAMattrRGline 'ID:ERR204916' 'SM:ERR204916' \
--quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD--quantTranscriptomeBan Singleend
if [ -f ERR204916.Unmapped.out.mate1 ]; then
mv ERR204916.Unmapped.out.mate1 ERR204916.unmapped_1.fastq
gzip ERR204916.unmapped_1.fastq
fi
if [ -f ERR204916.Unmapped.out.mate2 ]; then
mv ERR204916.Unmapped.out.mate2 ERR204916.unmapped_2.fastq
gzip ERR204916.unmapped_2.fastq
fi
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN":
star: $(STAR --version | sed -e "s/STAR_//g")
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
gawk: $(echo $(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*$//')
END_VERSIONS
Command exit status:
105
Command output:
STAR --genomeDir STARIndex --readFilesIn input1/ERR204916_1_val_1.fq.gz input2/ERR204916_2_val_2.fq.gz --runThreadN 12 --outFileNamePrefix ERR204916. --sjdbGTFfile genes_chrX.gtf --outSAMattrRGline ID:ERR204916 SM:ERR204916 --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributesNH HI AS NM MD --quantTranscriptomeBan Singleend
STAR version: 2.7.9a compiled: 2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
Jan 17 03:25:16 ..... started STAR run
Jan 17 03:25:16 ..... loading genome
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
STAR --genomeDir STARIndex --readFilesIn input1/ERR204916_1_val_1.fq.gz input2/ERR204916_2_val_2.fq.gz --runThreadN 12 --outFileNamePrefix ERR204916. --sjdbGTFfile genes_chrX.gtf --outSAMattrRGline ID:ERR204916 SM:ERR204916 --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributesNH HI AS NM MD --quantTranscriptomeBan Singleend
STAR version: 2.7.9a compiled: 2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
Jan 17 03:25:16 ..... started STAR run
Jan 17 03:25:16 ..... loading genome
EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a
SOLUTION: please re-generate genome from scratch with running version of STAR, or with version: 2.7.4a
Jan 17 03:25:16 ...... FATAL ERROR, exiting
Work dir:
/ceph_disk3/mengpf/work/Project/Nextflow/rnasplice/work/5b/2c86f21fb9af7fc6b71f96eac9a670
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '.nextflow.log' file for details
nextflow run rnasplice/main.nf \
--input samplesheet.csv \
--contrasts contrastsheet.csv \
--genome GRCh37 \
--outdir result \
-profile docker \
--fasta /ceph_disk3/mengpf/work/Project/Nextflow/rnasplice/data/ref/X.fa.gz \
--gtf /ceph_disk3/mengpf/work/Project/Nextflow/rnasplice/data/ref/genes_chrX.gtf \
--star_index /ceph_disk3/mengpf/work/Project/Nextflow/rnasplice/data/ref/STARIndex/
No response
No response
Running the pipeline with multiple contrasts in the contrast sheet results in multiple errors as mentioned in the filename. The pipeline runs fine with only one contrast at a time. As such, it's possible that this issue might be related to a separate report, which was focused on SUPPA: #71
Relevant input files, as well as the full log, are attached below.
nextflow run nf-core/rnasplice -r dev -latest -c custom.config -params-file params.yml --igenomes_ignore --genome null \
--input /data/share/santina-cutrupi/sample-sheet-rnasplice.csv \
--outdir test-rnasplice -profile docker --source genome_bam \
--fasta /data/share/santina-cutrupi/genome/gencode_v44_spike-ins.fasta \
--gtf /data/share/santina-cutrupi/genome/gencode_v44_spike-ins.gtf \
--star_index /data/share/santina-cutrupi/genome/index/star \
--salmon_index /data/share/santina-cutrupi/genome/index/salmon \
--rmats --rmats_read_len 100 --rmats_paired_stats \
--contrasts /data/share/santina-cutrupi/contrasts-rnasplice.csv \
--aligner star --dexseq_exon false --miso_genes "ENSG00000004961.15, ENSG00000005302.19, ENSG00000147403.18"
-[nf-core/rnasplice] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:RMATS:RMATS_POST (HepG2_TARDBP_TRT-HepG2_TARDBP_CTL)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:RMATS:RMATS_POST (HepG2_TARDBP_TRT-HepG2_TARDBP_CTL)` terminated with an error exit status (1)
Command executed:
mkdir -p HepG2_TARDBP_TRT-HepG2_TARDBP_CTL/rmats_post
rmats.py \
--gtf gencode_v44_spike-ins.gtf \
--b1 HepG2_TARDBP_TRT_bamlist.txt \
--b2 HepG2_TARDBP_CTL_bamlist.txt \
--od HepG2_TARDBP_TRT-HepG2_TARDBP_CTL/rmats_post \
--tmp HepG2_TARDBP_TRT-HepG2_TARDBP_CTL/rmats_temp \
-t paired \
--libType fr-unstranded \
--readLength 100 \
--variable-read-length \
--nthread 12 \
--tstat 12 \
--cstat 0.0001 \
--task post \
--paired-stats \
\
\
\
--allow-clipping \
1> HepG2_TARDBP_TRT-HepG2_TARDBP_CTL/rmats_post.log
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:RMATS:RMATS_POST":
rmats: $(echo $(rmats.py --version) | sed -e "s/v//g")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
HepG2_TARDBP_TRT_REP2_sorted.bam not found in .rmats files
HepG2_TARDBP_TRT_REP1_sorted.bam not found in .rmats files
HepG2_TARDBP_CTL_REP1_sorted.bam not found in .rmats files
HepG2_TARDBP_CTL_REP2_sorted.bam not found in .rmats files
Work dir:
/data/share/santina-cutrupi/work/44/1986fadc43abab0d325223ec214ee9
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`
-- Check '.nextflow.log' file for details
custom.config.txt
params.yml.txt
contrasts-rnasplice.csv.txt
sample-sheet-rnasplice.csv.txt
nextflow.log.txt
Nextflow 23.04.2
Latest Dev version of the rnasplice pipeline
The pipeline fails when running with --rmats
and the latest GTF file for human for Gencode: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.annotation.gtf.gz, even though --gencode
is specified in the command.
GTF file source: https://www.gencodegenes.org/human/
I'm including a command below that reproduces the error. The sample sheet and contrast sheet are based on the pipeline's test
profile, but I've customized the GTF and reference genome.
nextflow run nf-core/rnasplice -r dev -latest -profile docker --outdir test-small-rnasplice --gencode --genome GRCh38 \
--input https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/samplesheet/samplesheet.csv \
--contrasts https://raw.githubusercontent.com/nf-core/test-datasets/rnasplice/samplesheet/contrastsheet.csv \
--gtf https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.annotation.gtf.gz --rmats --rmats_read_len 75 --rmats_paired_stats --aligner star_salmon --dexseq_exon
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3` terminated with an error exit status (139)
Command executed:
gffread gencode.v43.annotation.gtf -L | awk -F' ' -vOFS=' ' '{ gsub("transcript", "mRNA", $3); print}' > gencode.v43.annotation_genes.gff3
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3":
gffread: $(gffread --version 2>&1)
END_VERSIONS
Command exit status:
139
Command output:
(empty)
Command error:
.command.sh: line 2: 28 Segmentation fault (core dumped) gffread gencode.v43.annotation.gtf -L
30 Done | awk -F' ' -vOFS=' ' '{ gsub("transcript", "mRNA", $3); print}' > gencode.v43.annotation_genes.gff3
No response
No response
I am running rnasplice using the STAR mapping, and Salmon output files from the nf-core rnaseq pipeline. I presume, if I implement this in the nf-params file, rnaplice can work with the rnaseq output. I am getting the following error:
Command error:
INFO: Converting SIF file to temporary sandbox...
WARNING: Skipping mount /home/lety/data/CBBI_Projects/general/software/miniconda3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Attaching package: 'DRIMSeq'
The following object is masked from 'package:base':
proportions
Error in .local(x, ...) :
min_samps_gene_expr >= 0 && min_samps_gene_expr <= ncol(x@counts) is not TRUE
Calls: <Anonymous> -> <Anonymous> -> .local -> stopifnot
Execution halted
INFO: Cleaning up image...
This is a similar error to the closed issue #69
Where running this pipeline through conda or docker solved the problem. However, I can not deviate from using singularity. Are there other options to solve this error?
A commenter suggested that this is a known STAR 2.7.10a issue.
How can we proceed with this issue?
nextflow \
run nf-core/rnasplice \
-r 1.0.0 \
-profile singularity \
--singularity_pull_docker_container \
-name $runname \
-params-file nf-params_rnasplice.json \
-resume
parameter file:
{
"fasta": "/data/CBBI_Projects/SNRPA_Function/processed/dgrashof/snrpa_function/dgrashof/Nextflow/RNAseq_Salmon/genomes/GRCm39.primary_assembly.genome.fa",
"gtf": "/data/CBBI_Projects/SNRPA_Function/processed/dgrashof/snrpa_function/dgrashof/Nextflow/RNAseq_Salmon/genomes/gencode.vM28.primary_assembly.annotation.gtf",
"gencode": true,
"save_reference": true,
"save_unaligned": true,
"save_align_intermeds": true,
"aligner": "star_salmon",
"extra_salmon_quant_args": "--incompatPrior 0.0",
"max_cpus": 30,
"skip_trimming": false,
"trim_nextseq": 25,
"deseq2_vst": true,
"max_memory": "60.GB",
"max_time": "168h",
"save_trimmed": true,
"pseudo_aligner": "salmon",
"skip_bigwig": false,
"skip_preseq": false,
"skip_qualimap": false,
"skip_dupradar": false,
"skip_biotype_qc": false,
"skip_markduplicates": false,
"rseqc_modules": "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication,tin"
}
No response
As referenced here #83
I am still stopped at this point:
run_stager.R CP_TG-CP_WT DEXSeqResults.CP_TG-CP_WT.tsv perGeneQValue.CP_TG-CP_WT.tsv dexseq
Error in
[<-(
tmp, idCon, 1, value = unlist(txLevelAdjustments)) : subscript out of bounds Calls: stageWiseAdjustment -> stageWiseAdjustment -> .local -> .stageWiseTest Execution halted
Any suggestion?
Best
nextflow run nf-core/rnasplice --input $wd/samplesheet_orig.csv \
--contrasts $wd/contrast.csv \
--outdir splice_Brain_TG_vs_Brain_WT \
--genome GRCm38 \
--aligner star_salmon \
--dexseq_exon true \
--min_samps_gene_expr 2 \
--min_samps_feature_expr 2 \
--min_gene_expr 5 \
--min_feature_expr 5 \
--min_feature_prop 0.2 \
--edger_exon true\
--rmats false \
--dexseq_dtu true \
--suppa true \
--suppa_per_local_event true \
--suppa_per_isoform true \
--save_reference true \
--sashimi_plot false \
-config $wd/config_HPC.config \
-profile docker \
-r dev
contrast.csv
nextflow.log
splicing_P107535352.log
N E X T F L O W ~ version 23.04.2
Launching https://github.com/nf-core/rnasplice
[hopeful_gilbert] DSL2 - revision: 9fe10b0 [dev]
Debian 10
I ran the pipeline through Tower and it keeps kicking back the error of my contrast sheet having no header. I ran just the checkcontrastsheet.py locally on the csv and it's giving the same error. It doesn't happen on Tower when I run it with the test data though. Not sure what to make of this. I'm just including the python I ran locally before because it 100% recapitulates the issue without having to run the whole pipeline.
ejennings@DESKTOP-C17P9CF Downloads % python check_contrastsheet.py contrast_test_share.csv testout
[CRITICAL] The given contrast sheet does not appear to contain a header.
This is the CSV I tested on:
contrast_test_share.csv
I'm using the pipeline, but I'm getting an error when trying to run it with my single-end data in the samplesheet file. I wanted to know if anyone has had a similar error and how you solved it please so you can explain it to me.
Thank you so much.
nextflow run nf-core/rnasplice --input samplesheet.csv --source fastq --contrasts contrastsheet.csv --outdir /home/fcr/proyecto_p1/parte2/results_RNAsplice4 --genome GRCh37 -profile docker
TERMINAL OUTPUT
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/rnasplice] Pipeline completed with errors-
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)` terminated with an error exit status (1)
Command executed:
check_samplesheet_fastq.py samplesheet.csv samplesheet.valid.csv
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:INPUT_CHECK:SAMPLESHEET_CHECK":
python: $(python --version | sed 's/Python //g')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
[CRITICAL] The sample sheet **must** contain these column headers: strandedness, fastq_2, sample, condition, fastq_1.
Work dir:
/home/fcr/proyecto_p1/parte2/work/12/d830cb6b9c9f0807c2a5da281ea1ad
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '.nextflow.log' file for details
This is my samplesheet.csv file:
sample,fastq_1,strandedness,condition
SRR10503052,/home/fcr/proyecto_p1/parte2/SRR10503052_1.fastq.gz,unstranded,BR0
SRR10503053,/home/fcr/proyecto_p1/parte2/SRR10503053_1.fastq.gz,unstranded,BR0
SRR10503054,/home/fcr/proyecto_p1/parte2/SRR10503054_1.fastq.gz,unstranded,BR0
SRR10503095,/home/fcr/proyecto_p1/parte2/SRR10503095_1.fastq.gz,unstranded,BR15
SRR10503096,/home/fcr/proyecto_p1/parte2/SRR10503096_1.fastq.gz,unstranded,BR15
SRR10503097,/home/fcr/proyecto_p1/parte2/SRR10503097_1.fastq.gz,unstranded,BR15
No response
Hey all, I had a package error: 'stager.R: subscript out of bounds.' when I was running rnasplice pipeline, it seems like stage-wise adjustment out of range in gene expression process. I'd be so thankful if anyone could provide some advices:
nextflow run nf-core/rnasplice --input --outdir -r dev --skip_alignment false --rmats true --dexseq_exon true --edger_exon true --dexseq_dtu true-profile singularity --
INFO: Converting SIF file to temporary sandbox...
WARNING: Skipping mount /home/yl/.conda/envs/nf-core/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'stageR'
The following object is masked from 'package:methods':
getMethod
Error in [<-
(*tmp*
, idCon, 1, value = unlist(txLevelAdjustments)) :
subscript out of bounds
Calls: stageWiseAdjustment -> stageWiseAdjustment -> .local -> .stageWiseTest
Execution halted
INFO: Cleaning up image...
Nextflow version (22.10.1)
256 cores 280GB
singularity
ubuntu 22.04
-r dev
When running the pipeline from FASTQ files, the user currently needs to specify the strandedness as one of unstranded
, forward
or reverse
, according to the documentation: https://nf-co.re/rnasplice/dev/docs/usage#samplesheet-input
It would be great to allow users to set this to auto
and have the pipeline be able to infer strandedness automatically, the way nf-core/rnaseq
does.
Here, $NXF_HOME
is set to /omics/groups/xxxxx/internal/xxxxx/.nextflow
.
miso_prefix
gets set to miso_prefix: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data
. Therefore, it looks for the output file /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188383_sorted
which doesn't exist, but the actual location should be in the working directory test_local
. Actually, the _sorted
directories are not created there.
(base) -bash-4.2$ ls test_local/misopy/miso_data/
ERR188383 ERR188428 ERR188454 ERR204916
Complete error:
-[nf-core/rnasplice] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (1)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (1)` terminated with an error exit status (1)
Command executed:
sashimi_plot --plot-event ENSG00000004961 index miso_settings.txt --output-dir sashimi
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI":
python: $(python --version | sed "s/Python //g")
misopy: $(python -c "import pkg_resources; print(pkg_resources.get_distribution('misopy').version)")
END_VERSIONS
Command exit status:
1
Command output:
Reading settings from: miso_settings.txt
Parsing data:bam_prefix
Parsing data:miso_prefix
Parsing data:bam_files
Parsing data:miso_files
Parsing plotting:fig_width
Parsing plotting:fig_height
Parsing plotting:intron_scale
Parsing plotting:exon_scale
Parsing plotting:logged
Parsing plotting:font_size
Parsing plotting:ymax
Parsing plotting:show_posteriors
Parsing plotting:bar_posteriors
Parsing plotting:number_junctions
Parsing plotting:resolution
Parsing plotting:posterior_bins
Parsing plotting:gene_posterior_ratio
Parsing plotting:colors
Parsing plotting:bar_color
Parsing plotting:bf_thresholds
miso_prefix: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data
Searching for MISO files in: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188383_sorted
- Looking for chromosome X directories
Error: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188383_sorted not a directory.
Error: Could not find MISO output files for sample ERR188383_sorted (after searching in /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188383_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188428_sorted
- Looking for chromosome X directories
Error: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188428_sorted not a directory.
Error: Could not find MISO output files for sample ERR188428_sorted (after searching in /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188428_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188454_sorted
- Looking for chromosome X directories
Error: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188454_sorted not a directory.
Error: Could not find MISO output files for sample ERR188454_sorted (after searching in /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188454_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR204916_sorted
- Looking for chromosome X directories
Error: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR204916_sorted not a directory.
Error: Could not find MISO output files for sample ERR204916_sorted (after searching in /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR204916_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Reading dimensions from settings...
- Height: 7.00
- Width: 7.00
Plotting read densities and MISO estimates along event...
- Event: ENSG00000004961
Setting up plot using dimensions: [7.0, 7.0]
Using intron scale 30.0
Using exon scale 4.0
Reading sample label: ERR188383_sorted.bam
Processing BAM: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/star/ERR188383_sorted.bam
Command error:
Parsing plotting:number_junctions
Parsing plotting:resolution
Parsing plotting:posterior_bins
Parsing plotting:gene_posterior_ratio
Parsing plotting:colors
Parsing plotting:bar_color
Parsing plotting:bf_thresholds
miso_prefix: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data
Searching for MISO files in: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188383_sorted
- Looking for chromosome X directories
Error: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188383_sorted not a directory.
Error: Could not find MISO output files for sample ERR188383_sorted (after searching in /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188383_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188428_sorted
- Looking for chromosome X directories
Error: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188428_sorted not a directory.
Error: Could not find MISO output files for sample ERR188428_sorted (after searching in /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188428_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188454_sorted
- Looking for chromosome X directories
Error: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188454_sorted not a directory.
Error: Could not find MISO output files for sample ERR188454_sorted (after searching in /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR188454_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR204916_sorted
- Looking for chromosome X directories
Error: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR204916_sorted not a directory.
Error: Could not find MISO output files for sample ERR204916_sorted (after searching in /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/misopy/miso_data/ERR204916_sorted and its subdirectories). Are you sure MISO output files are present in that directory?
Reading dimensions from settings...
- Height: 7.00
- Width: 7.00
Plotting read densities and MISO estimates along event...
- Event: ENSG00000004961
Setting up plot using dimensions: [7.0, 7.0]
Using intron scale 30.0
Using exon scale 4.0
Reading sample label: ERR188383_sorted.bam
Processing BAM: /omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/star/ERR188383_sorted.bam
Traceback (most recent call last):
File "/usr/local/bin/sashimi_plot", line 11, in <module>
sys.exit(main())
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/sashimi_plot.py", line 276, in main
plot_label=plot_label)
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/sashimi_plot.py", line 153, in plot_event
plot_label=plot_label)
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/plot_utils/plot_gene.py", line 698, in plot_density_from_file
plot_title=plot_title)
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/plot_utils/plot_gene.py", line 260, in plot_density
junction_log_base=junction_log_base)
File "/usr/local/lib/python2.7/site-packages/misopy/sashimi_plot/plot_utils/plot_gene.py", line 48, in plot_density_single
bamfile = pysam.Samfile(bam_filename, 'rb')
File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 950, in pysam.libcalignmentfile.AlignmentFile._open
IOError: [Errno 2] could not open alignment file `/omics/groups/xxxxx/internal/xxxxx/.nextflow/assets/nf-core/rnasplice/test_local/star/ERR188383_sorted.bam`: No such file or directory
Work dir:
/omics/odcf/analysis/xxxxx_projects/sb_tall_lines/nextflow/work/99/c923adb950181d6c7810fcdf94cecc
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
nextflow run nf-core/rnasplice -profile test -c local.config --outdir test_local -r dev
params {
config_profile_description = 'Deutsches Krebsforschungszentrum (DKFZ) HPC cluster profile provided by nf-core/configs'
config_profile_contact = 'Kübra Narcı [email protected]'
config_profile_name = 'DKFZ cluster'
max_cpus = 16
max_memory = '48.GB'
max_time = '48.h'
}
singularity {
enabled = true
autoMounts = true
}
process {
executor = 'local'
}
executor {
name = 'local'
cpus = 16
memory = '48 GB'
}
My aim was to run rnasplice to output results for SUPPA2. It is not clear whether the following is an error on my part, or there are no significant results. !No genes left after filtering! makes we think it is the latter, but your opinion would be welcome. I am happy to provide more information if it help.
Command line:
nextflow run nf-core/rnasplice --input samplesheet_fastqs_minus.csv --contrasts contrastsheet_minus.csv --outdir RNA-seq_fastqs_minus_samples -profile singularity -r 1.0.2 --rmats --source fastq --fasta Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa --gtf Saccharomyces_cerevisiae.R64-1-1.111.gtf --miso_genes <redacted> --aligner star_salmon --rmats_read_len 139
Output:
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)` terminated with an error exit status (1)
Command executed:
run_drimseq_filter.R salmon.merged.txi.dtu.rds tximport.tx2gene.tsv samplesheet_fastqs_minus.csv \
4 \
2 \
2 \
10 \
0.1 \
10
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER":
r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
bioconductor-drimseq: $(Rscript -e "library(DRIMSeq); cat(as.character(packageVersion('DRIMSeq')))")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
INFO: Converting SIF file to temporary sandbox...
WARNING: Skipping mount /usr/local/singularity-ce-3.11.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Attaching package: 'DRIMSeq'
The following object is masked from 'package:base':
proportions
Error in dmDS_filter(counts = x@counts, min_samps_gene_expr = min_samps_gene_expr, :
!No genes left after filtering!
Calls: <Anonymous> -> <Anonymous> -> .local -> dmDS_filter
Execution halted
INFO: Cleaning up image...
Work dir:
<redacted>/work/69/970b0a2cad7dab41066bb18623d068
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
-- Check '.nextflow.log' file for details
No response
nextflow version 23.04.1.5866, run locally on server
singularity container 3.11.2
Linux Ubuntu 22.04.3 LTS
nf-core/rnasplice 1.0.2
Could you share the example contrastsheet.csv
because the one provided is not working
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