tbrittoborges
commented
3 weeks ago The origin of the problem here is on this line: Wrote 0 clusters.. This means no clusters (splicing events) were selected. Which GTF/GFF annotation are you using? Is it the same you used to align the BAM files?
Hello everyone, I'm encountering an issue while running a Baltica workflow (version 1.2.4, python 3.7.12) with unstranded RNA-seq data. The execution halted at LeafCutter differential splicing analysis step. Here’s a summary of the error message:
Command: baltica all path/to/config.yaml - - use-singularity - -verbose - -cores 10
Select jobs to execute...
[Thu Oct 31 15:34:34 2024] rule leafcutter_differential_splicing: input: leafcutter/exons.gtf.gz, leafcutter/RGNEF-vs-CTR/RGNEF-vs-CTR_perind_numers.counts.gz, leafcutter/RGNEF-vs-CTR/diff_introns.txt output: leafcutter/RGNEF-vs-CTR/RGNEF-vs-CTR_cluster_significance.txt log: logs/leafcutter/leafcutter_differential_splicing/RGNEF-vs-CTR.log jobid: 0 reason: Missing output files: leafcutter/RGNEF-vs-CTR/RGNEF-vs-CTR_cluster_significance.txt wildcards: comp_names=RGNEF-vs-CTR threads: 10 resources: tmpdir=/tmp
Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 18 Rules claiming more threads will be scaled down. Select jobs to execute... Activating singularity image /home/cappelli/.baltica/singularity/2f0497e2227c782b99d020de15ba0db2.simg /bin/bash: /root/.bashrc: Permission denied Loading counts from leafcutter/RGNEF-vs-CTR/RGNEF-vs-CTR_perind_numers.counts.gz Loading metadata from leafcutter/RGNEF-vs-CTR/diff_introns.txt Encoding as CTR =0, RGNEF =1 Settings: $output_prefix [1] "leafcutter/RGNEF-vs-CTR/RGNEF-vs-CTR" $max_cluster_size [1] Inf $min_samples_per_intron [1] 2 $min_samples_per_group [1] 2 $min_coverage [1] 5 $timeout [1] 30 $num_threads [1] 10 $exon_file [1] "leafcutter/exons.gtf.gz" $init [1] "smart" $seed [1] 12345 $help [1] FALSE
Running differential splicing analysis... [Thu Oct 31 15:34:36 2024] Error in rule leafcutter_differential_splicing: jobid: 0 input: leafcutter/exons.gtf.gz, leafcutter/RGNEF-vs-CTR/RGNEF-vs-CTR_perind_numers.counts.gz, leafcutter/RGNEF-vs-CTR/diff_introns.txt output: leafcutter/RGNEF-vs-CTR/RGNEF-vs-CTR_cluster_significance.txt log: logs/leafcutter/leafcutter_differential_splicing/RGNEF-vs-CTR.log (check log file(s) for error details) shell:
Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-10-31T153434.446038.snakemake.log<<
From the RGNEF-vs-CTR.log I got this: Loading required package: Rcpp Loading required package: doMC Loading required package: foreach Loading required package: iterators Loading required package: parallel Error in
colnames<-(*tmp*, value = c("chr", "start", "end", "clu")) : attempt to set 'colnames' on an object with less than two dimensions Calls: differential_splicing -> get_intron_meta -> colnames<- Execution haltedPlus, also the intron_clustering.log reported a strange output: scanning /home/cappelli/Desktop/Baltica_RGNEF/leafcutter/CTR_1.junc... scanning /home/cappelli/Desktop/Baltica_RGNEF/leafcutter/CTR_2.junc... scanning /home/cappelli/Desktop/Baltica_RGNEF/leafcutter/CTR_3.junc... scanning /home/cappelli/Desktop/Baltica_RGNEF/leafcutter/RGNEF_1.junc... scanning /home/cappelli/Desktop/Baltica_RGNEF/leafcutter/RGNEF_2.junc... scanning /home/cappelli/Desktop/Baltica_RGNEF/leafcutter/RGNEF_3.junc... Parsing...
Wrote 0 clusters.. Split into 0 clusters... Sorting /home/cappelli/Desktop/Baltica_RGNEF/leafcutter/CTR_1.junc.. Sorting /home/cappelli/Desktop/Baltica_RGNEF/leafcutter/CTR_2.junc.. Sorting /home/cappelli/Desktop/Baltica_RGNEF/leafcutter/CTR_3.junc.. Sorting /home/cappelli/Desktop/Baltica_RGNEF/leafcutter/RGNEF_1.junc.. Sorting /home/cappelli/Desktop/Baltica_RGNEF/leafcutter/RGNEF_2.junc.. Sorting /home/cappelli/Desktop/Baltica_RGNEF/leafcutter/RGNEF_3.junc.. merging 6 junction files... merging 6 files done.
I am not sure if it is an upstream input file problem (I used an annotation.gtf file converted from gff3 using Agat) cause I checked the format and seems to be correct.
Any insights or suggestions would be greatly appreciated! Thank you for your help!
Alessandra