ablab
Spades hammer error
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
params.txt
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
- [X] Yes
Hello
Likely your input reads are corrupted. I would suggest you to perform some QC steps.
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: @.***>
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
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: @.***>
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.
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.
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