Error: Failed to create thread.

Cheng Long

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Jul 28, 2024, 7:29:58 PM7/28/24

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Hi Sam,

Thank you for your nice pipeline!

After installing, when I run both master_script_for_sample_file.bash and test_of_master_script_tiny.bash, I got the same error.

#CPU threads: 64
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
#Target sequences to report alignments for: 1
Temporary directory: ./
Opening the database... [9.91399s]
Opening the input file... [0.00156s]
Opening the output file... [0.022887s]
Loading query sequences... [0.00556s]
Running complexity filter... [0.010321s]
Building query histograms... [0.014297s]
Allocating buffers... [0.003s]
Loading reference sequences... [55.0843s]
Building reference histograms... [9.00006s]
Error: Failed to create thread.
'/scratch/clong2/samsa2/programs/diamond blastx --db /scratch/clong2/samsa2/full_databases/RefSeq_bac -q /home/clong2/scratch/samsa2/output/step_3_output/control_1_TINY.merged.ribodepleted.fastq -a /home/clong2/scratch/samsa2/output/step_3_output/control_1_TINY.merged.ribodepleted.fastq.RefSeq -t ./ -k 1' exited with non-zero status 1

Can you please help me with this!Thank you very much!

Regards,

Cheng

Sam Westreich

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Jul 29, 2024, 4:02:40 PM7/29/24

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Hi Cheng,

Where are you running this? This looks like a local system error (the execution doesn't have permission to create a new CPU thread).

A search showed a similar error from another bioinformatics associated group when the user was operating on a shared machine: https://groups.google.com/g/plink2-users/c/rm_ULNhSOFg?pli=1

Is it possible to try this again and potentially allocate more memory?

Best,

Sam

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Sam Westreich, PMP, PhD

Microbiome Scientist, DNAnexus

https://www.dnanexus.com

Andrew Forgie

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Jul 29, 2024, 4:26:36 PM7/29/24

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Hi Cheng and Sam,

From what I remember the master script will not work on compute Canada because of permissions.

I’ll have to check my scripts. The directories need to be customized depending on where they are in your scratch folder and you have to work in your scratch folder (gets deleted every month or so keep a backup).

I broke down the master script into 3 parts to run on compute Canada. That being said, there may be another work around with compute Canada with requesting cpu or permission as Sam has stated.

Cheers,

Andrew

On Jul 29, 2024, at 5:02 PM, Sam Westreich <swest...@gmail.com> wrote:

To view this discussion on the web visit https://groups.google.com/d/msgid/samsa-bioinformatics-group/CAJgADcKmLTqc42c%2BGttKTk2i0QmkyrpZhbDdWWNCpFkD_afNDQ%40mail.gmail.com.

Cheng Long

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Jul 29, 2024, 11:50:27 PM7/29/24

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Hi Andrew and Sam,

Thanks for your reply, I ran in Compute Canada,

I used your three steps scripts, Andrew, when ran the Step 1, it worked, But when I ran Step2, it got the same error.

So, do you all think it is a system? Then I will contact Compute Canada to ask for more resources.

Regards,

Cheng

Andrew Forgie

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Jul 31, 2024, 3:36:11 PM7/31/24

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Might have to load diamond to compute Canada.?

Should be able to type in diamond —version or something to see what is loaded.

I had to use v2.0.2 to create and run diamond database on cc.

On Jul 30, 2024, at 12:50 AM, Cheng Long <lomgch...@gmail.com> wrote:

Hi Andrew and Sam,

To view this discussion on the web visit https://groups.google.com/d/msgid/samsa-bioinformatics-group/ea945525-61d5-4e2e-a11f-a61e97368d28n%40googlegroups.com.

Incredible Budget

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Jan 8, 2025, 12:23:25 AM1/8/25

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