RENEE GUI error #230
Description
Error: RENEE GUI opens a window showing the dry run. But on clicking 'OK' button on dry-run window, the next window does not pop-up that prompts the user to submit the slurm job.
HPC OnDemand Graphical session terminal output:
-bash-4.4$ sinteractive --tunnel --time=12:00:00 --mem=8gb --cpus-per-task=4
salloc: Pending job allocation 64198545
salloc: job 64198545 queued and waiting for resources
module load ccbrpipelinersalloc: job 64198545 has been allocated resources
salloc: Granted job allocation 64198545
salloc: Waiting for resource configuration
salloc: Nodes cn0050 are ready for job
module load ccbrpipeliner
Created 1 generic SSH tunnel(s) from this compute node to
biowulf for your use at port numbers defined
in the $PORTn ($PORT1, ...) environment variables.
Please create a SSH tunnel from your workstation to these ports on biowulf.
On Linux/MacOS, open a terminal and run:
ssh -L 45359:localhost:45359 jailwalapa@biowulf.nih.gov
For Windows instructions, see https://hpc.nih.gov/docs/tunneling
bash-4.4$ module load ccbrpipeliner
[+] Loading ccbrpipeliner 8 ...
###########################################################################
CCBR Pipeliner release 8
###########################################################################
"ccbrpipeliner" is a suite of end-to-end pipelines and tools
Visit https://github.com/CCBR for more details.
Pipelines are available on BIOWULF and FRCE.
Tools are available on BIOWULF, HELIX and FRCE.
The following pipelines/tools will be loaded in this module:
PIPELINES:
ASPEN v1.1 ATAC-seq https://ccbr.github.io/ASPEN/1.1
CARLISLE v2.7 CUT&RUN https://ccbr.github.io/CARLISLE/2.7
CHAMPAGNE v0.5 ChIP-seq https://ccbr.github.io/CHAMPAGNE/0.5
CHARLIE v0.12 circRNAs https://ccbr.github.io/CHARLIE/0.12
CRISPIN v1.2 CRISPR https://ccbr.github.io/CRISPIN/1.2
ESCAPE v1.2 EV-seq https://ccbr.github.io/ESCAPE/1.2
LOGAN v0.3 whole genome seq https://ccbr.github.io/LOGAN/0.3
RENEE v2.7 bulk RNA-seq https://ccbr.github.io/RENEE/2.7
SINCLAIR v0.3 scRNA-seq https://ccbr.github.io/SINCLAIR/0.3
XAVIER v3.2 whole exome-seq https://ccbr.github.io/XAVIER/3.2
TOOLS:
spacesavers2 v0.14 https://ccbr.github.io/spacesavers2/
permfix v0.6 https://github.com/ccbr/permfix/
ccbr_tools v0.4 https://ccbr.github.io/Tools/
###########################################################################
Thank you for using CCBR Pipeliner
Comments/Questions/Requests:
CCBR_Pipeliner@mail.nih.gov
###########################################################################
bash-4.4$ renee gui
[+] Loading singularity 4.2.2 on cn0050
[+] Loading snakemake 7.32.4
Python version: 3.11.12
/data/CCBR_Pipeliner/db/PipeDB/Conda2025/envs/py3.11-8/lib/python3.11/argparse.py:2084: ResourceWarning: unclosed <socket.socket fd=3, family=2, type=1, proto=0, laddr=('0.0.0.0', 0)>
for action, arg_count in zip(positionals, arg_counts):
ResourceWarning: Enable tracemalloc to get the object allocation traceback
RENEE (v2.7.1)
{'hg19_19': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/hg19_19.json', 'hg19_36': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/hg19_36.json', 'hg38_30': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/hg38_30.json', 'hg38_34': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/hg38_34.json', 'hg38_36': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/hg38_36.json', 'hg38_38': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/hg38_38.json', 'hg38_41': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/hg38_41.json', 'hg38_45': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/hg38_45.json', 'hg38_48': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/hg38_48.json', 'mCalJac1_2021': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/mCalJac1_2021.json', 'mm10_M21': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/mm10_M21.json', 'mm10_M23': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/mm10_M23.json', 'mm10_M25': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/mm10_M25.json', 'mm39_M36': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/mm39_M36.json', 'mm39_M37': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/mm39_M37.json', 'mmul10_108': '/vf/users/CCBR_Pipeliner/Pipelines/RENEE/.v2.7.1/config/genomes/biowulf/mmul10_108.json'}
['hg19_19', 'hg19_36', 'hg38_30', 'hg38_34', 'hg38_36', 'hg38_38', 'hg38_41', 'hg38_45', 'hg38_48', 'mCalJac1_2021', 'mm10_M21', 'mm10_M23', 'mm10_M25', 'mm39_M36', 'mm39_M37', 'mmul10_108']
layout is ready!
window created!
--SUBMIT-- {'--INDIR--': '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs', 'Browse': '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs', '--OUTDIR--': '/data/CCRCCDI/analysis/ccrtegs45/parthav_test', 'Browse0': '/data/CCRCCDI/analysis/ccrtegs45/parthav_test', '--ANNOTATION--': 'hg38_48'}
['/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/10_NTC_CAR52F_A_S18_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/10_NTC_CAR52F_A_S18_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/11_NTC_CAR52F_B_S19_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/11_NTC_CAR52F_B_S19_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/12_NTC_CAR52F_C_S20_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/12_NTC_CAR52F_C_S20_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/13_NTC_CAR53M_A_S21_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/13_NTC_CAR53M_A_S21_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/14_NTC_CAR53M_B_S22_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/14_NTC_CAR53M_B_S22_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/15_NTC_CAR53M_C_S23_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/15_NTC_CAR53M_C_S23_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/16_SPKO_CAR40F_A_S24_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/16_SPKO_CAR40F_A_S24_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/17_SPKO_CAR40F_B_S2_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/17_SPKO_CAR40F_B_S2_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/18_SPKO_CAR40F_C_S4_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/18_SPKO_CAR40F_C_S4_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/19_SPKO_CAR52F_A_S6_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/19_SPKO_CAR52F_A_S6_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/1_NTC_A_S1_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/1_NTC_A_S1_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/20_SPKO_CAR52F_B_S8_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/20_SPKO_CAR52F_B_S8_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/21_SPKO_CAR52F_C_S10_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/21_SPKO_CAR52F_C_S10_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/22_SPKO_CAR53M_A_S12_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/22_SPKO_CAR53M_A_S12_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/23_SPKO_CAR53M_B_S14_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/23_SPKO_CAR53M_B_S14_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/24_SPKO_CAR53M_C_S16_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/24_SPKO_CAR53M_C_S16_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/2_NTC_B_S3_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/2_NTC_B_S3_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/3_NTC_C_S5_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/3_NTC_C_S5_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/4_SPPL3KO_A_S7_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/4_SPPL3KO_A_S7_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/5_SPPL3KO_B_S9_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/5_SPPL3KO_B_S9_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/6_SPPL3KO_C_S11_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/6_SPPL3KO_C_S11_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/7_NTC_CAR40F_A_S13_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/7_NTC_CAR40F_A_S13_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/8_NTC_CAR40F_B_S15_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/8_NTC_CAR40F_B_S15_R2_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/9_NTC_CAR40F_C_S17_R1_001.fastq.gz', '/data/CCRCCDI/analysis/ccrtegs45/raw_data/fastqs/9_NTC_CAR40F_C_S17_R2_001.fastq.gz']
^[c
