Spades hammer error

[zafranulhaq12]

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

• Yes

[asl]

Hello

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

[zafranulhaq12]

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 <#1387 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BLYVYH6V6Y2AHU23GTFPP2LZZQXGHAVCNFSM6AAAAABPHFKFTGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOBZGI3DMMBYG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[asl]

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]

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 <#1387 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BLYVYH2TKD5SMPOA4FHDQILZ2F2D7AVCNFSM6AAAAABPHFKFTGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJVGUZDIMZVG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[AmaliT]

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]

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]

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