no abyss-pe.Makefile acess denied

[Sabrin2020]

error after running my data with abyss-pe using slurm script, test data works fine

- [ ] version of ABySS with abyss-pe version abyss-pe (ABySS) 2.3.5

- [ ] distribution of Linux with lsb_release -d (abyss) [asga9989@hpcl001 trim]$ lsb_release -d Description: Red Hat Enterprise Linux Server release 7.2 (Maipo)

Assembly error

Loaded 3030000 reads into Bloom filter Loaded 3040000 reads into Bloom filter Loaded 3044782 reads from trim800.2u.fastq into Bloom filter Bloom filter FPR: 0.000542% Counting Bloom filter stats: #counters = 238609294272 #size (B) = 238609294272 threshold = 2 popcount = 3562650019 FPR = 4.97e-06% terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc bash: line 1: 5165 Aborted abyss-stack-size 65536 abyss-bloom-dbg -k90 -q3 -v -b250G -j24 trim300_1.1p.fastq trim300_1.2p.fastq trim300_2.1p.fastq trim300_2.2p.fastq trim500.1p.fastq trim500.2p.fastq trim800.1p.fastq trim800.2p.fastq trim300_1.1u.fastq trim300_1.2u.fastq trim300_2.1u.fastq trim300_2.2u.fastq trim500.1u.fastq trim500.2u.fastq trim800.1u.fastq trim800.2u.fastq > Hypoplectrus-1.fa make: *** [Hypoplectrus-1.fa] Error 134

• [ ] complete abyss-pe command line abyss-pe k=90 name=Hypoplectrus B=250G v=-v j=24 lib='lib1 lib2 lib3 lib4'
  lib1='trim300_1.1p.fastq trim300_1.2p.fastq' lib2='trim300_2.1p.fastq trim300_2.2p.fastq' lib3='trim500.1p.fastq trim500.2p.fastq' lib4='trim800.1p.fastq trim800.2p.fastq'
  se='trim300_1.1u.fastq trim300_1.2u.fastq trim300_2.1u.fastq trim300_2.2u.fastq trim500.1u.fastq trim500.2u.fastq trim800.1u.fastq trim800.2u.fastq'

[lcoombe]

Hi Sabrin,

I also responded to your google issue, but thank you for including more information here. We do monitor both methods of communication, but issues via github (only) is preferable. You are using a rather old ABySS version - I'd first suggest updating your installation to the most recent release. In addition, I recommend testing your installation with our small test: https://github.com/bcgsc/abyss#assemble-a-small-synthetic-data-set

Hope that helps - thank you for your interest in ABySS! Lauren

[Sabrin2020]

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[Sabrin2020]

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[lcoombe]

Hello @Sabrin2020,

So to be clear, the test data ran OK the first time, but not the second? Had you made any adjustments to your conda environment (installed any other tools, deactivated it, adjusted your path again, etc.)? What exact command did you run each time?

On our end, we can best help you troubleshoot if we have the full information (command used, full log, ABySS version, etc)

[Sabrin2020]

test data works after server admins installed latest version of abyss.

[lcoombe]

Great, glad to hear that the test data is working for you now!

It looks like you've edited your original comment with an updated log. How much memory do you have on the machine that you're running ABySS on? That error often comes up if ABySS runs out of memory.

Just as a note - please do avoid editing previous comments to remove what you said or substantially change the content. It's helpful for other users to see how you encountered and resolved the problems.

[github-actions[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your interest in ABySS!