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mahulchak / quickmerge

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
GNU General Public License v3.0
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Program runs, but doesn't provide correct output #73

Open drew-olson-tmru opened 1 year ago

drew-olson-tmru commented 1 year ago

Hi,

I am trying to use this tool merge a hifiasm and a canu assembly, but I am running into some issues. The jobs seem to complete, but they are really short and I only end up with the delta files and two .fa files: hybrid_oneline.fa self_oneline.fa. Not sure what the issue is. I have made sure that the assemblies stay either hybrid or self in the positional arguments. My script is:

merge_wrapper.py -l 2136987 -p $OUTDIR/31242 $hifiasm/31242.hifiasm.racon.fixed.fasta $canuasm/31242.canu.racon.fixed.fasta

I am really confused why I am only getting 31242.delta 31242.rq.delta hybrid_oneline.fa self_oneline.fa as the results. Can someone help me with this?

mahulchak commented 1 year ago

It seems quickmerge is not running. Can you check if quickmerge is in your path?

On Wed, Jul 5, 2023, 5:41 AM drew-olson-tmru @.***> wrote:

Hi,

I am trying to use this tool merge a hifiasm and a canu assembly, but I am running into some issues. The jobs seem to complete, but they are really short and I only end up with the delta files and two .fa files: hybrid_oneline.fa self_oneline.fa. Not sure what the issue is. I have made sure that the assemblies stay either hybrid or self in the positional arguments. My script is:

merge_wrapper.py -l 2136987 -p $OUTDIR/31242 $hifiasm/31242.hifiasm.racon.fixed.fasta $canuasm/31242.canu.racon.fixed.fasta

I am really confused why I am only getting 31242.delta 31242.rq.delta hybrid_oneline.fa self_oneline.fa as the results. Can someone help me with this?

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/mahulchak/quickmerge/issues/73__;!!CzAuKJ42GuquVTTmVmPViYEvSg!KxvJ3QI_XsyjtBdufrBRdapV-w4kI76mYVLr9l3bTZbo7JM8or_Gi0CTMacvmOvNwPUslOTZyHEgiX2gAxlaiMYL$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABZQH2C7RIGTWMTXM56UN5TXOSWLRANCNFSM6AAAAAAZ6HU5GY__;!!CzAuKJ42GuquVTTmVmPViYEvSg!KxvJ3QI_XsyjtBdufrBRdapV-w4kI76mYVLr9l3bTZbo7JM8or_Gi0CTMacvmOvNwPUslOTZyHEgiX2gA5FlSeUV$ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

drew-olson-tmru commented 1 year ago

When I “echo $PATH”, I get:

/software/el9/apps/gcc/12.2.0/bin:/software/el9/apps/quickmerge/0.3/quickmerge-0.3:/software/el9/apps/quickmerge/0.3/quickmerge-0.3/MUMmer3.23:/software/el9/apps/quickmerge/0.3/quickmerge-0.3/merger:... (rest of my PATH here)

So, it looks like it is in the PATH. I may just need to reach out to the people running our HPC.

Drew Olson Biological Sciences Technician USDA, ARS, SEA U.S. National Poultry Research Center Toxicology & Mycotoxin Research Unit 950 College Station Rd Athens, GA 30605 Email: @.**@.> Phone: 706-546-3613

Ph.D. Student Department of Plant Pathology University of Georgia, Athens, GA 30602

[signature_3788834368]

From: Mahul Chakraborty @.> Date: Wednesday, July 5, 2023 at 6:20 AM To: mahulchak/quickmerge @.> Cc: Olson, Drew - REE-ARS @.>, Author @.> Subject: Re: [mahulchak/quickmerge] Program runs, but doesn't provide correct output (Issue #73) It seems quickmerge is not running. Can you check if quickmerge is in your path?

On Wed, Jul 5, 2023, 5:41 AM drew-olson-tmru @.***> wrote:

Hi,

I am trying to use this tool merge a hifiasm and a canu assembly, but I am running into some issues. The jobs seem to complete, but they are really short and I only end up with the delta files and two .fa files: hybrid_oneline.fa self_oneline.fa. Not sure what the issue is. I have made sure that the assemblies stay either hybrid or self in the positional arguments. My script is:

merge_wrapper.py -l 2136987 -p $OUTDIR/31242 $hifiasm/31242.hifiasm.racon.fixed.fasta $canuasm/31242.canu.racon.fixed.fasta

I am really confused why I am only getting 31242.delta 31242.rq.delta hybrid_oneline.fa self_oneline.fa as the results. Can someone help me with this?

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/mahulchak/quickmerge/issues/73__;!!CzAuKJ42GuquVTTmVmPViYEvSg!KxvJ3QI_XsyjtBdufrBRdapV-w4kI76mYVLr9l3bTZbo7JM8or_Gi0CTMacvmOvNwPUslOTZyHEgiX2gAxlaiMYL$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABZQH2C7RIGTWMTXM56UN5TXOSWLRANCNFSM6AAAAAAZ6HU5GY__;!!CzAuKJ42GuquVTTmVmPViYEvSg!KxvJ3QI_XsyjtBdufrBRdapV-w4kI76mYVLr9l3bTZbo7JM8or_Gi0CTMacvmOvNwPUslOTZyHEgiX2gA5FlSeUV$ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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