PICARD_MERGESAMFILES processes stuck indefinitely, no error logs #507
Description
PICARD_MERGESAMFILES processes stuck indefinitely, no error logs
Description
The nf-core/chipseq pipeline runs smoothly until reaching the PICARD_MERGESAMFILES step, then tasks hang in RUNNING status permanently.
No error messages, no OOM, no crashes, no progress updates. CPU and memory resources are sufficient, but the process never completes.
Command used
nextflow run nf-core/chipseq
-profile singularity
--input /home/XXX/CHIP/data/sample.csv
--outdir /home/XXX/CHIP/result
--fasta /home/XXX/CHIP/data/GCA_000513815.1_TrireRUTC30_1_genomic.fna.gz
--gtf /home/XXX/CHIP/data/GCA_000513815.1_TrireRUTC30_1_genomic.gtf.gz
--narrow_peak
--macs_pvalue 0.005
--min_reps_consensus 2
--macs_gsize 32681481
--save_reference
--max_cpus 48
--max_memory 128.GB
Nextflow.log snippet (stuck tasks)
Apr-03 16:49:06.716 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 2 -- submitted tasks are shown below
~> TaskHandler[id: 54; name: NFCORE_CHIPSEQ:CHIPSEQ:PICARD_MERGESAMFILES (24_Ip_REP1); status: RUNNING; exit: -; error: -; workDir: /home/XXX/work/bd/c09414286584491ed1147164f90511]
~> TaskHandler[id: 53; name: NFCORE_CHIPSEQ:CHIPSEQ:PICARD_MERGESAMFILES (24_Ip_REP2); status: RUNNING; exit: -; error: -; workDir: /home/XXX/work/94/76dfaaa10d2124e70eccc289516a4e]
The monitor prints the same message repeatedly every 5 minutes, no changes.
Environment
- CPU: Intel(R) Xeon(R) Gold 6530 (x86_64, 64 cores)
- RAM: 251 GiB
- OS: Linux
- Run: Nextflow + Singularity
- Conda env: nfchipseq
Sample sheet (corrected version)
sample,fastq_1,fastq_2,replicate,antibody,control,control_replicate
24_Ip,/home/XXX/CHIP/data/24_1_Ip_1.fq.gz,/home/XXX/CHIP/data/24_1_Ip_2.fq.gz,1,MY_ANTIBODY,24_Input,1
24_Ip,/home/XXX/CHIP/data/24_2_Ip_1.fq.gz,/home/XXX/CHIP/data/24_2_Ip_2.fq.gz,2,MY_ANTIBODY,24_Input,2
36_Ip,/home/XXX/CHIP/data/36_1_Ip_1.fq.gz,/home/XXX/CHIP/data/36_1_Ip_2.fq.gz,1,MY_ANTIBODY,36_Input,1
36_Ip,/home/XXX/CHIP/data/36_2_Ip_1.fq.gz,/home/XXX/CHIP/data/36_2_Ip_2.fq.gz,2,MY_ANTIBODY,36_Input,2
24_Input,/home/XXX/CHIP/data/24_1_Input_1.fq.gz,/home/XXX/CHIP/data/24_1_Input_2.fq.gz,1,,,
24_Input,/home/XXX/CHIP/data/24_2_Input_1.fq.gz,/home/XXX/CHIP/data/24_2_Input_2.fq.gz,2,,,
36_Input,/home/XXX/CHIP/data/36_1_Input_1.fq.gz,/home/XXX/CHIP/data/36_1_Input_2.fq.gz,1,,,
36_Input,/home/XXX/CHIP/data/36_2_Input_1.fq.gz,/home/XXX/CHIP/data/36_2_Input_2.fq.gz,2,,,