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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Spades hammer error #1387

Open zafranulhaq12 opened 1 month ago

zafranulhaq12 commented 1 month ago

Description of bug

when i run command for genome assembly spades. py -1 (forward seq) -2 (reverse seq) -o output_directory after sometimes running it shows this error

"== Error == system call for: "['/usr/libexec/spades/spades-hammer', '/media/comsats/c18a94ad-d4b7-4f58-b90f-2e6bd5d58092/Zafran/B3/spades_output/corrected/configs/config.info']" finished abnormally, OS return value: -6 None"

spades.log

spades.log

params.txt

params.zip

SPAdes version

v3.15.5

Operating System

Ubuntu 24.04.1 LTS

Python Version

No response

Method of SPAdes installation

manual

No errors reported in spades.log

asl commented 1 month ago

Hello

Likely your input reads are corrupted. I would suggest you to perform some QC steps.

zafranulhaq12 commented 1 month ago

Can you tell me what QC steps I have to perform?

On Wed, Oct 2, 2024 at 10:52 PM Anton Korobeynikov @.***> wrote:

Hello

Likely your input reads are corrupted. I would suggest you to perform some QC steps.

— Reply to this email directly, view it on GitHub https://github.com/ablab/spades/issues/1387#issuecomment-2389266087, or unsubscribe https://github.com/notifications/unsubscribe-auth/BLYVYH6V6Y2AHU23GTFPP2LZZQXGHAVCNFSM6AAAAABPHFKFTGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOBZGI3DMMBYG4 . You are receiving this because you authored the thread.Message ID: @.***>

asl commented 1 month ago

Can you tell me what QC steps I have to perform?

I'd suggest you to ensure that sequence lines in FASTQ match the quality lines

zafranulhaq12 commented 1 month ago

how is it possible? can you refer me to some tutorials?

On Sun, Oct 6, 2024 at 10:51 PM Anton Korobeynikov @.***> wrote:

Can you tell me what QC steps I have to perform?

I'd suggest you to ensure that sequence lines in FASTQ match the quality lines

— Reply to this email directly, view it on GitHub https://github.com/ablab/spades/issues/1387#issuecomment-2395524357, or unsubscribe https://github.com/notifications/unsubscribe-auth/BLYVYH2TKD5SMPOA4FHDQILZ2F2D7AVCNFSM6AAAAABPHFKFTGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJVGUZDIMZVG4 . You are receiving this because you authored the thread.Message ID: @.***>

AmaliT commented 1 month ago

Hi @asl

I am getting the same error here. I have tried starting fresh and have QC checked the fastq files as well and I dont see any issues with the input files as it runs through smoothly through tools like fastqc/stats wrapper bbtools. Are you able to advise what else might be causing this error?

Attached is the log.

spades.log

asl commented 1 month ago

I am getting the same error here. I have tried starting fresh and have QC checked the fastq files as well and I dont see any issues with the input files as it runs through smoothly through tools like fastqc/stats wrapper bbtools. Are you able to advise what else might be causing this error?

Do you not hijack other issues as your issue might be entirely different (and actually it is), open a new one.

AmaliT commented 4 weeks ago

I am getting the same error here. I have tried starting fresh and have QC checked the fastq files as well and I dont see any issues with the input files as it runs through smoothly through tools like fastqc/stats wrapper bbtools. Are you able to advise what else might be causing this error?

Do you not hijack other issues as your issue might be entirely different (and actually it is), open a new one.

ok, sorry. Thanks