Segmentation fault error ending Seq2Fun run prematurely

Seq2Fun
,
1

Hello,
I have been working on running a few data sets of FASTQ files for species without annotated genomes through Seq2Fun using Docker Desktop. I have successfully run one species, and though I experienced one failure, it succeeded on the second attempt. However, when trying to run the second species, the run has failed 3 times. I am able to begin the run, it accepts the metadata and pathways, and gets through 8-12 of the 24 samples before stopping. It stops at a different point each time.

I am inputting the fastq.gz files, and running on fish orthologs (fishes_v2.0.fmi and fishes_annotation_v2.0). I am using the dockerxialab/expressanalyst_docker:latest image, created 3 months ago. The runs are set to use 12 threads, with all other settings left at default.

Is it a matter of just re-starting the run until it succeeds, or is there some other trouble-shooting I can try?

When checking the job_logs, the errors are as follows:
/data//Users/Katie/BowRiverFormatted/SS/RESULTS/results_2024_04_02_15_24_34/ExecuteRawSeq.sh: line 3: 253 Segmentation fault /home/software/Seq2Fun/bin/seq2fun --longlog --sampletable /data//Users/Katie/BowRiverFormatted/SS/RESULTS/results_2024_04_02_15_24_34/sampleTable.txt --tfmi

/data//Users/Katie/BowRiverFormatted/SS/RESULTS/results_2024_04_01_06_27_11/ExecuteRawSeq.sh: line 3: 275 Segmentation fault /home/software/Seq2Fun/bin/seq2fun --longlog --sampletable /data//Users/Katie/BowRiverFormatted/SS/RESULTS/results_2024_04_01_06_27_11/sampleTable.txt --tfmi

/data//Users/Katie/BowRiverFormatted/SS/RESULTS/results_2024_04_01_21_43_48/ExecuteRawSeq.sh: line 3: 262 Segmentation fault /home/software/Seq2Fun/bin/seq2fun --longlog --sampletable /data//Users/Katie/BowRiverFormatted/SS/RESULTS/results_2024_04_01_21_43_48/sampleTable.txt --tfmi

Cheers!
Katie

Files below:

image
image1634×852 13.2 KB

2

Most likely related to your computing environment, not the Docker itself. What is the memory and CPU available for the computing? "…The runs are set to use 12 threads ". Have you tried to set to 4 threads?

3

Hi Jeff,
Thanks for the response. I am running an Intel i5-12600K and the physical memory is 80GB of DDR5. Following your response I started a new run using only 4 threads, and experienced another failure with the following error:

/data//Users/Katie/BowRiverFormatted/SS/RESULTS/results_2024_04_05_04_27_24/ExecuteRawSeq.sh: line 3: 259 Segmentation fault /home/software/Seq2Fun/bin/seq2fun --longlog --sampletable /data//Users/Katie/BowRiverFormatted/SS/RESULTS/results_2024_04_05_04_27_24/sampleTable.txt --tfmi

Please let me know if there’s any other information I can provide you.

Thanks!
Katie