terminated with an error exit status (140)

[Shaileshdesai76]

Hii,
I am running eager latest version, installed through conda, and its working fine with for low number of reads data.

However when i am running for large data, despite the increase of resource and running mode as slurm, its still not able to process the file.

I get the error like;

[73/e6e607] NOTE: Process bwa (B_S_NHMD_231146) terminated with an error exit status (140) -- Execution is retried (3)
[dd/f66caa] NOTE: Process bwa (TOG_XPCJ_T2_GAGAAG_L001_R1_001.fastq.gz) terminated with an error exit status (140) -- Execution is retried (3)

i feel this is because of taking long times.

i have also made config file, like this,
cat nextflow.config
process {
executor = 'slurm'
cpus = 30
memory = '250 GB'
time = '60h'
}

process {

withName: 'EAGER:ALIGN_BWA:BWA_ALN' {
cpus = 20
memory = 200.GB
time = 58.h
}

withName: 'EAGER:ALIGN_BWA:BWA_SE' {
cpus = 20
memory = 200.GB
time = 58.h
}
}

i feel it is being accepted by nexftflow, because there is no error in log file.

my data is single end and size around 50-60 Gb.

I look forward for help.

[TCLamnidis]

Hi @Shaileshdesai76

Exit code 140 typically indicates that a process was terminated due to exceeding resource limits, such as memory, disk space, or time constraints, especially in environments like SLURM or SGE. This often suggests that the job needs more resources allocated to it to run successfully.

You can have a look into the execution trace (which is saved within the output directory under pipeline_info/ to see the peak usage of your failing jobs and adjust your configuration accordingly.

For troubleshooting help, you can also reach out to us in the dedicated #eager channel on the nf-core slack space: https://nf-co.re/join

[Shaileshdesai76]

Hi Thisease, Thank you for your quick reponse.

i check those, file, but i think those which are failed, not showing the memory requirement.
i am just showing the two lines for inspections.

67 6d/d60a93 10921279 bwa (TOG_XPCJ_B1_CTCTAG_L001_R1_001.fastq.gz) COMPLETED 0 2025-11-25 18:16:48.859 9h 35m 35s 6h 50m 32s 1101.7% 13.2 GB 14.2 GB 555.5 GB 12.9 GB
68 73/e6e607 10921280 bwa (B_sauveli_NHMD_231146) FAILED 140 2025-11-25 18:16:58.398 14h 44m 26s 11h 59m 6s -- - - -
69 dd/f66caa 10921281 bwa (TOG_XPCJ_T2_GAGAAG_L001_R1_001.fastq.gz) FAILED 140 2025-11-25 18:16:58.435 14h 44m 56s 11h 59m 36s - - - - -

[TCLamnidis]

Ah! right. You will then need to look into your slurm log files to see the reason for the job being cancelled. It should mention what resource limit was exceeded there.

9 times out of 10, you just need to give it more memory though.

[Shaileshdesai76]

Hii, i am sorry for late response, but i was waiting to job finish.
Well it ended again with same error,

i have attached two files, for your inspection, and importantly despite giving more memory and resource, pipeline_report says only 125 GB memory, i am not sure this is because of that. one more thing as i believe by default eager or nextflow gives 4 hours for each job, if it fail next 8 hours and again if fails it gives 16 hours , so my job getting finish exactly at 16 h, hence my nextflow configure file is not properly working i think.

My job log err file contain nothing, but out file is attached below.

I look foraward for your help.

execution_trace_2025-11-24_19-29-49.txt
pipeline_report.txt