Regarding of interop_index-summary result

Illumina / interop

C++ Library to parse Illumina InterOp files

http://illumina.github.io/interop/index.html

GNU General Public License v3.0

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Regarding of interop_index-summary result #277

Closed hmkim closed 2 years ago

hmkim commented 2 years ago

Hi!

Using interop_index-summary, I got the result.

but this result had only lane 2 information.

In my case, Is it correct or run information was lost?

Thank you in advance!

"./" means run directory.

$ interop_index-summary --csv=1 ./

Screen Shot 2021-10-06 at 9 57 56 AM

In SAV, I can show the index metrics per lane normally. but I can't get the output in CLI (interop_index-summary) Maybe this metrics require samplesheet for separating lane in run directory.

ezralanglois commented 2 years ago

I cannot say what the issue is. I tried this with the latest version and it worked fine on a 2 lane NS2K run.

What version of InterOp are you using? The v3.0.35-src is a fallback for code compiled outside of version control.

hmkim commented 2 years ago

I'll check it again after compiling of git repo. I installed it via conda. (https://anaconda.org/bioconda/illumina-interop)

hmkim commented 2 years ago

This run have multiple lane information. (Please check the sample sheet!) Screen Shot 2021-10-15 at 4 33 32 PM

With latest version, (# Version: v1.1.23) it was same.

Screen Shot 2021-10-15 at 4 32 57 PM

ezralanglois commented 2 years ago

SAV shows all 4 lanes? and not like the above?

hmkim commented 2 years ago

SAV shows all 4 lanes? and not like the above?

@ezralanglois Yes, SAV shows all 4 lanes.

ezralanglois commented 2 years ago

Can you provide the indexmetricsout.bin? That would help to dig more into this issue.

Thanks, Rob

hmkim commented 2 years ago

Can you provide the indexmetricsout.bin? That would help to dig more into this issue.

Thanks, Rob

Thank you!

IndexMetricsOut.bin.zip

ezralanglois commented 2 years ago

Thanks, could you provide TileMetricsOut.bin too? Also the RunInfo.xml?

Sorry, I forgot that I need those two files to load everything properly in the same way you do.

I am pretty certain this is a bug, but I need to determine what is being done in SAV that is wrong in the public library.

hmkim commented 2 years ago

Archive.zip

Please check this!

Tell me if you need anything

ezralanglois commented 2 years ago

Thanks!

ezralanglois commented 2 years ago

I loaded the InterOp in SAV and I see the following All Lanes Lane 1, 2 and 4

Lane 3

This is consistent with what I see in the InterOp file too. There is only lane 3 data present.

So unless I misunderstood something, everything looks to be working as expected. The IndexMetricsOut.bin just does not contain the information expected.

hmkim commented 2 years ago

Oops. so I'll check the file size between a and b server.

a server is on windows .

b server is another linux server . so I had the issue in b server. I'll check the copying work is normal or not

Thank you very much for your inspection.

hmkim commented 2 years ago

I'm really thank you for your inspection.

Maybe I confused

Yesterday, my colleague in lab checked this flowcell run.

As you checked, we are confirmed same result. There is only lane 3 data present.

I have another question.

Will IndexMetricsOut.bin be created after demultiplexing step ?

ezralanglois commented 2 years ago

Yes, bclconvert or bcl2fastq or whatever does the demultiplexing will produce this file.

hmkim commented 2 years ago

maybe.. at that time, my colleague would have been working on it for lane 3 only.