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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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problem running SPAdes error -11 #1191

Open tmms345 opened 1 year ago

tmms345 commented 1 year ago

Description of bug

Hi, When I try to run my assembly it gives me this error:

== Error == system call for: "['/home/name/salmo/SPAdes-3.15.4-Linux/bin/spades-hammer', '/home/name/salmo/Spades_out_dir/ISZ-2_S5/corrected/configs/config.info']" finished abnormally, OS return value: -11

I tried running on both linux and WSL, but with the same result and I tried also with conda.

spades2.log is from linux spades1.log in from WSL

params.txt is from linux

spades.log

spades2.log spades1.log

params.txt

params.txt

SPAdes version

SPAdes-3.15.4-Linux

Operating System

Ubuntu 22.04.3 LTS

Python Version

Python 3.9.12

Method of SPAdes installation

Binaries, Conda

No errors reported in spades.log

asl commented 1 year ago

How much free RAM is available for your SPAdes job?

tmms345 commented 1 year ago

How I can check it, to be sure? Probably 2 GB

Il giorno mer 4 ott 2023 alle 20:24 Anton Korobeynikov < @.***> ha scritto:

How much free RAM is available for your SPAdes job?

— Reply to this email directly, view it on GitHub https://github.com/ablab/spades/issues/1191#issuecomment-1747420317, or unsubscribe https://github.com/notifications/unsubscribe-auth/BC733YSQMM42VXBRYGWCUQTX5WSVBAVCNFSM6AAAAAA5TBEMW2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBXGQZDAMZRG4 . You are receiving this because you authored the thread.Message ID: @.***>

robertwhbaldwin commented 1 year ago

everyone is posting these errors to the board. You need to compile spades your self using spades_compile.py and it will work fine.

asl commented 1 year ago

How I can check it, to be sure? Probably 2 GB

I doubt that this is enough amount for anything non-trivial

tmms345 commented 1 year ago

Sorry I don’t understand, I have to run this command?

Il giorno mer 4 ott 2023 alle 22:03 robertwhbaldwin < @.***> ha scritto:

everyone is posting these errors to the board. You need to compile spades your self using spades_compile.py and it will work fine.

— Reply to this email directly, view it on GitHub https://github.com/ablab/spades/issues/1191#issuecomment-1747556764, or unsubscribe https://github.com/notifications/unsubscribe-auth/BC733YWL4KSJRHMTUYUAC5TX5W6JJAVCNFSM6AAAAAA5TBEMW2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBXGU2TMNZWGQ . You are receiving this because you authored the thread.Message ID: @.***>

tmms345 commented 1 year ago

Yes, but I tried with another pc, 8Gb RAM, and I obtained the same result

Il giorno mer 4 ott 2023 alle 22:08 Anton Korobeynikov < @.***> ha scritto:

How I can check it, to be sure? Probably 2 GB

I doubt that this is enough amount for anything non-trivial

— Reply to this email directly, view it on GitHub https://github.com/ablab/spades/issues/1191#issuecomment-1747564687, or unsubscribe https://github.com/notifications/unsubscribe-auth/BC733YW3RZM3LSDMY2MHY43X5W63JAVCNFSM6AAAAAA5TBEMW2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBXGU3DINRYG4 . You are receiving this because you authored the thread.Message ID: @.***>

robertwhbaldwin commented 1 year ago

How are you installing spades on your computer? Are you using the pre-compiled binaries or are you compiling it your self ?

tmms345 commented 1 year ago

What do you mean by pre-compiled?

Il giorno mer 4 ott 2023 alle 22:38 robertwhbaldwin < @.***> ha scritto:

How are you installing spades on your computer? Are you using the pre-compiled binaries or are you compiling it your self ?

— Reply to this email directly, view it on GitHub https://github.com/ablab/spades/issues/1191#issuecomment-1747604578, or unsubscribe https://github.com/notifications/unsubscribe-auth/BC733YTZWX2TY2HJ3SWACXDX5XCLXAVCNFSM6AAAAAA5TBEMW2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBXGYYDINJXHA . You are receiving this because you authored the thread.Message ID: @.***>

tmms345 commented 1 year ago

I think Pre-compiled, because I copied and posted on my bash

Il giorno mer 4 ott 2023 alle ore 22:38 robertwhbaldwin < @.***> ha scritto:

How are you installing spades on your computer? Are you using the pre-compiled binaries or are you compiling it your self ?

— Reply to this email directly, view it on GitHub https://github.com/ablab/spades/issues/1191#issuecomment-1747604578, or unsubscribe https://github.com/notifications/unsubscribe-auth/BC733YTZWX2TY2HJ3SWACXDX5XCLXAVCNFSM6AAAAAA5TBEMW2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBXGYYDINJXHA . You are receiving this because you authored the thread.Message ID: @.***>

Arthurdyu commented 11 months ago

the same problem！

Arthurdyu commented 11 months ago

Have you solved this error? really appreciate ！