/gs10 no longer avaiable on Biowulf ... container binding affected! #110
Description
Description of the bug
From: Cornejo Castro, Elena Maria (NIH/NCI) [C] elenamaria.cornejocastro@nih.gov
Date: Tuesday, December 16, 2025 at 12:02 PM
To: NCI CCBR_Pipeliner CCBR_Pipeliner@mail.nih.gov
Subject: CCBR LOGAN error help
Hello all,
I am attempting to run the CCBR LOGAN WGS pipeline on Biowulf, however it has failed multiple times.
My setup:
Step1: Initilalization
logan init
--output /data/cornejocastroe/aKS_WGS_HAMB/logan_output
Step2: stub-run
logan run
--output /data/cornejocastroe/aKS_WGS_HAMB/logan_output
--mode local -profile ci_stub
--genome hg38
--ffpe
--indelrealign
--sample_sheet /data/cornejocastroe/aKS_WGS_HAMB/hs_13117.txt
--fastq_input "/data/cornejocastroe/aKS_WGS_HAMB/WGS_raw/*R{1,2}.fastq.gz"
-stub --vc --sv --cnv
The error:
[2_SI_22_7464_A_13_S2_vs_3_13117_041917_S3, 2_SI_22_7464_A_13_S2, 3_13117_041917_S3]
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'ALIGN:matchbed (1)'
Caused by:
Process ALIGN:matchbed (1) terminated with an error exit status (255)
Command executed:
awk -F '\t' '{printf("%s\t0\t%s\n",$1,$2);}' /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/bwamem2/GRCh38.d1.vd1.fa.fai >temp.bed
bedtools intersect -a hg38_v0_wgs_calling_regions.hg38.bed -b temp.bed > target.bed
Command exit status:
255
Command output:
(empty)
Command error:
WARNING: Not virtualizing pid namespace by configuration
WARNING: While bind mounting '/vf/users:/vf/users': destination is already in the mount point list
WARNING: While bind mounting '/gs11:/gs11': destination is already in the mount point list
WARNING: While bind mounting '/gs12:/gs12': destination is already in the mount point list
WARNING: While bind mounting '/spin1:/spin1': destination is already in the mount point list
WARNING: While bind mounting '/fdb:/fdb': destination is already in the mount point list
WARNING: While bind mounting '/gpfs:/gpfs': destination is already in the mount point list
WARNING: skipping mount of /gs10: stat /gs10: no such file or directory
FATAL: container creation failed: mount /gs10->/gs10 error: while mounting /gs10: mount source /gs10 doesn't exist
Work dir:
/vf/users/cornejocastroe/aKS_WGS_HAMB/logan_output/work/ae/2d2912fef14d619fe9284cd61ae74e
Container:
/data/CCBR_Pipeliner/SIFS/dnousome-ccbr_logan_base-v0.3.9.img
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh
-- Check '.nextflow.log' file for details
My SINGULARITY_BINDPATH and APPTAINER_BINDPATH are empty, which makes me thinks it could come from the system Singularity configuration or is based on a setup error on my side.
I have attached the nextflow.config. If there is anything else I could provide to help identify the issue please let me know.
Many thanks,
Elena
Elena Maria Cornejo Castro, Ph.D. [c]
Scientist I, Viral Oncology Section
AIDS and Cancer Virus Program (ACVP)
Frederick National Laboratory for Cancer Research
National Institutes of Health
Building 535, Room 428
Office: 301-846-5828
ecornejo@nih.gov
Command used and terminal output
# Step1: Initilalization
logan init \
--output /data/cornejocastroe/aKS_WGS_HAMB/logan_output
# Step2: stub-run
logan run \
--output /data/cornejocastroe/aKS_WGS_HAMB/logan_output \
--mode local -profile ci_stub \
--genome hg38 \
--ffpe \
--indelrealign \
--sample_sheet /data/cornejocastroe/aKS_WGS_HAMB/hs_13117.txt \
--fastq_input "/data/cornejocastroe/aKS_WGS_HAMB/WGS_raw/*R{1,2}.fastq.gz" \
-stub --vc --sv --cnvRelevant files
No response
System information
No response