Open Riczury opened 4 months ago
Hi, thanks for reporting this. We will look in to it. In the meantime you may like to try the workflow again but with a different path for sample_sheet.csv and reference annotation files that do not contain a space eg. /mnt/c/Users/juanj/Desktop/maestria ric/Sample_sheet.csv
.
We do try to make all of our workflows work for paths where there is a space but it can still be the source of some errors.
Thank you very much, I just did what you recommended but the same error keeps coming up.
Would you mind sharing your sample sheet? Sample_sheet.csv
and if possible if you click 'open folder' in the app of the workflow - it should open a folder and there you will find a directory /work/a5/4b904ddecf39decedf9000e952c1f9
in the de_analysis folder there should be a counts.tsv
file - does it contain counts, if possible could you share that?
Sure, here is a picture. I tried to upload the files but says that it doesn't accept that format. And this is the sample sheet Samplesheet.csv I'll be happy to provide more information if needed to resolve the issue.
hmm that all looks fine, would you be able to share either your input RNAseq_transcriptome.fas
and genomic.gff3
- you can put them in a zip folder to share via github or if not cp and paste just a small section of each of the files or confirm that the references used in each match
and if you open any of those transcript_counts.tsv they contain counts against the records?
Sure here you have. And I can't open transcript_counts.tsv files they are empty Anotacion_y_Transcriptoma_ref.zip
Hey, so in the precomputed mode the references used in the gff need to match up with the references in the ref_annotation (the first column) - i didn't find eg. RNAseq_batch_1.2.1
in the reference annotation.
I didn't do i. I tried do it but this happened.
/mnt/c/Users/juanj/epi2melabs/workflows/epi2me-labs/wf-transcriptomes/main.nf
[DE1] DSL2 - revision: 3ecc85aafe
|||||||||| ____ _ __ _
|||||||||| | _| _ | | \/ | __| | | | |
||||| | | | |) | | ) | |\/| | _| ___| |/ ` | ' \/ |
||||| | |_| /| | / /| | | | |_|| | (| | |) _ \
|||||||||| |____|_| |_|___|| ||| ||\,|._/|/
|||||||||| wf-transcriptomes v1.2.1If you use epi2me-labs/wf-transcriptomes for your analysis please cite:
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Doing reference based transcript analysis
[32/812557] Submitted process > fastcat (1)
[e2/707924] Submitted process > pipeline:getVersions
[cf/263520] Submitted process > pipeline:getParams
[d7/5d6235] Submitted process > pipeline:preprocess_ref_annotation
[9a/c6ea05] Submitted process > pipeline:build_minimap_index (1)
[c4/812bb8] Submitted process > pipeline:collectFastqIngressResultsInDir (1)
[14/9d3fc5] Submitted process > pipeline:reference_assembly:map_reads (1)
[02/254241] Submitted process > pipeline:split_bam (1)
[cc/aaaa42] Submitted process > pipeline:assemble_transcripts (1)
ERROR ~ Error executing process > 'pipeline:assemble_transcripts (1)'
Caused by:
Process pipeline:assemble_transcripts (1)
terminated with an error exit status (1)
Command executed:
stringtie --rf -G amended.anotacion.gff2 -L -v -p 4 --conservative -o cDNA_batch_1.gff -l cDNA_batch_1 cDNA_batch_1.bam 2>/dev/null
Command exit status:
1
Command output:
(empty)
Work dir:
/mnt/c/Users/juanj/epi2melabs/instances/wf-transcriptomes_01J4S7H51523WSG4XGFD1EJHX1/work/cc/aaaa42547138f24a2a1fea2ffe6fa9
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
-- Check '/mnt/c/Users/juanj/epi2melabs/instances/wf-transcriptomes_01J4S7H51523WSG4XGFD1EJHX1/nextflow.log' file for details
Sorry i misunderstood what you have tried? The workflow has only really been set up to work and tested on the ref_annotation and ref_transcriptomes files from ncbi and ensemble. Is your ref_transcriptome a custom file? And where did you get the ref_annotation file from?
Hi, I used all the transcriptome sequences I obtained and a reference genome I downloaded from NCBI to run the transcriptome workflow to do the precomputed. From there I obtained the ref_transcriptome file. Then I tried to do the analysis using the sequences, the ref_annotation file I downloaded from NCBI, the ref_transcriptome I obtained and the sample sheet.
could you link me so i can try them?
Sure https://drive.google.com/drive/folders/17cSn6-CHiHt-QeuhOZSAQlTcyPp-UHvg?usp=drive_link Those are the documents that I used to do the analysis.
I am sorry for the delay - did you get it to work in the end? I can't access that link but could be that its expired as its been a while.
Operating System
Windows 10
Other Linux
No response
Workflow Version
v1.2.1
Workflow Execution
EPI2ME Desktop (Local)
Other workflow execution
No response
EPI2ME Version
v5.1.14
CLI command run
epi2me-labs/wf-transcriptomes v1.2.1.
Workflow Execution - CLI Execution Profile
standard (default)
What happened?
I want to do a differential expression analysis but I can't because it gives me this error.
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
no
Other demo data information
No response