liulab-dfci/rima_pipeline

rima_pipeline's Issues

Skip read alignment.

Hi, thanks for this tool.
I was wondering whether I can skip read alignment step and directly perform gene quantification and DEG analysis, which are all I want to do. This way, I can save a lot of time and resources.
Thanks again!

Job killed before alignment is finished

Hi there, thank you for the great and detailed package!

I was wondering if you could help me resolve an error with the pipeline where the process is killed before STAR alignment is finished. I am running this on a cluster so maybe the issue is the reference to usr/bin/bash?

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job counts:
count jobs
15 Downsampling_HouseKeeping
1 STAR_matrix
15 Size_downsampling
15 align_bam_stat
15 bam_downsampling
1 batch_removal
15 cdr3_preprocess
1 deseq2_differential_genes
15 gene_body_cvg_qc
1 gsea_plot
15 index_bam
15 junction_saturation
1 merge_bcr_clonality
1 merge_bcr_infil
1 merge_bcr_process
1 merge_bcr_shm
1 merge_tcr_clonality
1 merge_tcr_infil
1 merge_tcr_process
1 pca_sample_clustering
1 plot_gene_body_cvg
15 read_distrib_qc
1 read_distrib_qc_matrix
1 salmon_matrix
15 salmon_quantification
15 ss_bcr_process
15 ss_tcr_process
1 ssgsea
15 star_align
1 target
15 tin_score
1 tin_summary
1 trust4_cohort_plot
15 trust4_repertoire
1 volcano_plot
245

[Tue Aug 9 14:44:38 2022]
Job 23: Running STAR Alignment on s6234

STAR --runThreadN 64 --genomeDir /orange/brusko/leeanapeters/RIMA/ref_files/v22 --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 12 -$
Aug 09 14:44:38 ..... started STAR run
Aug 09 14:44:38 ..... loading genome
/usr/bin/bash: line 1: 9346 Killed STAR --runThreadN 64 --genomeDir /orange/brusko/leeanapeters/RIMA/ref_files/v22 --outReadsUnmapped No$
[Tue Aug 9 14:46:04 2022]
Error in rule star_align:
jobid: 23
output: analysis/star/s6234/s6234.unsorted.bam, analysis/star/s6234/s6234.sorted.bam, analysis/star/s6234/s6234.transcriptome.bam, analysis/star/s6234$
log: logs/star/s6234.star_align.log (check log file(s) for error message)
shell:
STAR --runThreadN 64 --genomeDir /orange/brusko/leeanapeters/RIMA/ref_files/v22 --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhang$
(exited with non-zero exit code)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /orange/brusko/leeanapeters/RIMA/RIMA_pipeline/.snakemake/log/2022-08-09T144412.563019.snakemake.log
3.16user 87.63system 1:59.21elapsed 76%CPU (0avgtext+0avgdata 26050936maxresident)k
97291464inputs+592outputs (1major+6594049minor)pagefaults 0swaps

There is no output in the star alignment log.

Any help would be appreciated!

Leeana

function "get.bcr.cluster.classswitch " has not been used

Dear, I am wondering how to get Ig isotype frequency as your tutorial, I guess to run get.bcr.cluster.classswitch funtion in trust4_bcr_process.R? Thank you so much!

MissingInputException

hello

running the following command resulted in the following error:

~/RIMA_pipeline$ snakemake -s RIMA.snakefile -np
Building DAG of jobs...
MissingInputException in line 96 of modules/mutation/mutation_cohort.snakefile:
Missing input files for rule fusion_plot:
analysis/batchremoval/tpm.genesymbol.batchremoved.csv

SHM Output Issue

Hello, I have been trying to use the Immune_repertoire portion of the RIMA pipeline to calculate SHM statistics for TRUST4 output mouse data (that has not otherwise been processed through the RIMA pipeline).

Rscript src/immune_repertoire/trust4_bcr_process.R --cdr3 C1.processed.txt -s test -o out

However, when I run trust4_bcr_process.R, the program fails with

[1] "Saving SHM results ..."
Error in if (is.na(sample_bcr_cluster)) { : the condition has length > 1
Execution halted

Commenting out that section of the code shown below allows it to run to completion, but I am worried about the effect on the validity of the data analysis.

} else if (is.na(sample_bcr_cluster)) {
ss.ratio <- NULL

Do you have any suggestions for fixing this?

Also, what is the actual statistic being calculated for the SHMRatio output? I am trying to make sure I understand what the values being outputted mean.

Thank you for your time and help, and happy holidays.

Job Execution failed during RSEQC stage

I have installed the package as detailed in the Tutorial of RNA-seq tumor immunity analysis using Google Cloud Platform on my institute’s HPC. The pipeline completes the star aligning, salmon and down sampling on the house keeping genes. But fails when running the tin_score, read_distrib_qc and junction_saturation jobs from RSEQC. I have included the .snakemake.log files which detail the errors. I have tried with different fastq files and the pipeline fails at the same stage. Any assistance would be greatly appreciated.
2023-12-04T152042.960586.snakemake.log
RIMA_Error_Log.txt

input data sample for hla_oncoplot()

Hi I want to apply the function you kindly provided, but was running into some issues of using my own data, probably due to the format. Can you please provide an example data for meta and expression data? Also, is the expression data necessary?

Thanks a lot!

'NoneType' object is not iterable

Good afternoon, thank you very much for making the tool available. I have installed RIMA following the GitHub tutorial (AWS), I have the following error when trying to run

snakemake -s RIMA.snakefile -np

InputFunctionException in line 129 of /mnt/panfs1/scratch/wsspaces/svalpione-tide-0/RIMA/RIMA_pipeline/RIMA.snakefile:
Error:
TypeError: 'NoneType' object is not iterable
Wildcards:

Traceback:
File "/xxx/RIMA/RIMA_pipeline/RIMA.snakefile", line 99, in all_targets
File "/xxx/RIMA/RIMA_pipeline/./modules/preprocess/preprocess_individual.snakefile", line 30, in preprocess_individual_targets

Any help please?
Thank you in advance

SV