Comments (11)
Hello @IanCodes
Would you mind re-running the pipeline with the following configuration:
min_samps_gene_expr: 0
min_gene_expr: 0
min_samps_feature_expr: 0
min_feature_expr: 0
min_samps_feature_prop: 0
min_feature_prop: 0
These parameters should effectively stop any filtering. If you still encounter the same issue, let me know and I can take a deeper look.
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Hello @jma1991,
Thank you for your reply and apologies for the delayed response.
I ran the following command line:
nextflow run nf-core/rnasplice --input samplesheet_fastqs_minus.csv --contrasts contrastsheet_minus.csv --outdir RNA-seq_fastqs_minus_samples_MINSIG -profile singularity -r 1.0.2 --source fastq --fasta Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa --gtf Saccharomyces_cerevisiae.R64-1-1.111.gtf --aligner star_salmon --rmats false --suppa true --dexseq_exon false --dexseq_dtu false --sashimi_plot false --edger_exon false --min_samps_gene_expr 0 --min_gene_expr 0 --min_samps_feature_expr 0 --min_feature_expr 0 --min_samps_feature_prop 0 --min_feature_prop 0
But I still got an error:
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 \
0 \
0 \
0 \
0 \
0 \
0
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/44/6b45b957ccdafc9f5e93c4b0b7cc34
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
This may or may not be related, but I cannot reproduce results obtained from the stand-alone rMATS-turbo (4.2) with rnasplice. The summary file of the stand-alone shows:
EventType EventTypeDescription TotalEventsJC TotalEventsJCEC SignificantEventsJC SigEventsJCSample1HigherInclusion SigEventsJCSample2HigherInclusion SignificantEventsJCEC SigEventsJCECSample1HigherInclusion SigEventsJCECSample2HigherInclusion
SE skipped exon 22132 22465 756 385 371 841 436 405
A5SS alternative 5' splice sites 10382 10438 168 94 74 185 109 76
A3SS alternative 3' splice sites 13738 13777 332 190 142 346 191 155
MXE mutually exclusive exons 2204 2243 74 24 50 82 26 56
RI retained intron 6764 6926 364 199 165 407 233 174
Summary of rnasplice are all zeros.
The command line with the stand-alone was:
rmats.py --gtf Mus_musculus.GRCm39.106.gtf --b1 WT.txt --b2 mutAff.txt --libType fr-firststrand --readLength 90 --variable-read-length --novelSS --nthread 4 --od wt-mutRev_rMATsOUT --tmp wt-mutRev-rMATsTMP
For rnasplice I used:
nextflow run nf-core/rnasplice --input samplesheet.csv --contrasts contrastsheet.csv --outdir Rev_vs_Normal_Ens106_default_sig -profile singularity -r 1.0.2 --source genome_bam --fasta Mus_musculus.GRCm39.dna.primary_assembly.fa --gtf Mus_musculus.GRCm39.106.gtf --aligner star --rmats_read_len 90 --rmats --rmats_novel_splice_site true --dexseq_exon false --dexseq_dtu false --sashimi_plot false --edger_exon false
The samplesheet was:
sample,condition,genome_bam,strandedness
N1,Normal,1295_521_2_510_S31_L005-vsHsap_Aligned.sortedByCoord.sorted.bam,reverse
N2,Normal,1395_721_1_510_S30_L005-vsHsap_Aligned.sortedByCoord.sorted.bam,reverse
N3,Normal,711_2_3_1295_115_HT_S32_L005-vsHsap_Aligned.sortedByCoord.sorted.bam,reverse
N4,Normal,711_6_1293_113_HT_S33_L005-vsHsap_Aligned.sortedByCoord.sorted.bam,reverse
N5,Normal,7_129_115_HT_S34_L005-vsHsap_Aligned.sortedByCoord.sorted.bam,reverse
N6,Normal,722_1_511_HT_S35_L005-vsHsap_Aligned.sortedByCoord.sorted.bam,reverse
R1,Rev,3131_3_K27_511_HT_S39_L005-vsHsap_Aligned.sortedByCoord.sorted.bam,reverse
R2,Rev,3150_2_512_HT_S40_L005-vsHsap_Aligned.sortedByCoord.sorted.bam,reverse
R3,Rev,3158_11_514_HT_S42_L005-vsHsap_Aligned.sortedByCoord.sorted.bam,reverse
R4,Rev,R27_3139_4_512_HT3_S41_L005-vsHsap_Aligned.sortedByCoord.sorted.bam,reverse
Sorry to dump this one here. I can restart a separate thread if that helps.
Thank you.
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H! I am having the same problem.
Did you finally solve it?
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@SergioManzano10 I haven't had a response. I will use the standalone tool for the time being.
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@SergioManzano10 I haven't had a response. I will use the standalone tool for the time being.
Apologies for the lack of progress on this issue. Is it possible to host your input files somewhere I can download and run locally? It's quite difficult for me to debug when the full test data seems to pass without issue.
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Not me because are clinical/private data, but maybe @IanCodes can.
It would be so helpful!
- Maybe the problem is that all quantifications methods are set to true and it crashes, or that the default value for the aligner is star_salmon? These are just ideas...
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@SergioManzano10 see https://github.com/Xinglab/rmats-turbo
from rnasplice.
@jma1991 I have an urgent deadline this week and a conference next week. When I get back i'll look into sourcing the files to you. I had to delete them last week to make space, so they need retrieving again. I'll also need permission to send them. I think Dropbox is probably the best route for me. If that works for you could you private message me, here, an email address to send the link.
EDIT:
I was easily able to get the files again, so if you can let me have contact details I can share them this week. Thanks.
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@jma1991 I have an urgent deadline this week and a conference next week. When I get back i'll look into sourcing the files to you. I had to delete them last week to make space, so they need retrieving again. I'll also need permission to send them. I think Dropbox is probably the best route for me. If that works for you could you private message me, here, an email address to send the link.
No problem, enjoy the conference. I'm not sure how to direct message on GitHub, but you can reach me on the nf-core Slack channel. Alternatively, if you have some public data that you used with the workflow and encountered the error, I can download it from SRA.
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EDIT: I was easily able to get the files again, so if you can let me have contact details I can share them this week. Thanks.
That's great, please send an email to [email protected] when you have availability.
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Related Issues (20)
- make contrasts file names consistent with those of the differentialabundance pipeline HOT 1
- Missing rMATS arguments HOT 2
- DEXSeq-DTU Stager pScreenAdjusted HOT 1
- sashimi_plot error HOT 2
- contrast file problem? HOT 7
- EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a HOT 2
- MISO error HOT 3
- The processes for splitting files are running very slowly with large numbers of input samples HOT 5
- Error: suppa_split_file.R Input_file must contain samplesheet samples. HOT 2
- Error in DRIMSeq::dmDSdata(counts = counts, samples = samps) HOT 3
- Error single-end execution HOT 1
- Error in SUPPA: Clustergroups are assigned incorrectly HOT 4
- Miso error HOT 8
- `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DEXSEQ_DTU (1)` HOT 7
- RNA splice output
- Merged genes output HOT 3
- DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER not working with special characters in sample names
- AWSmegatests are failing
- Spare memory for samtools issue
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