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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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error while parsing GFA path record #1342

Open IanDMedeiros opened 1 month ago

IanDMedeiros commented 1 month ago

Description of bug

binspreader threw an error while parsing assembly_graph_with_scaffolds.gfa. It looks like there are semicolons where the program was expecting tabs. I did not modify the assembly graph in any way after the assembly.

spades.log

binspreader.60.log

There was no spades.log file I can find from this run. I am attaching the log output from the hpc job.

params.txt

There was no params.txt file for this run.

SPAdes version

4.0.0

Operating System

Linux Rocky 8.9

Python Version

3.11.4

Method of SPAdes installation

binaries

No errors reported in spades.log

asl commented 1 month ago

You need to use the latest BinSPreader that is capable of reading GFA v1.2 files. Alternatively, if upgrading BinSPreader is not an option, you can emit graphs in old GFA v1.1 format via --gfa11 option.

See https://ablab.github.io/spades/output.html#gfa for more information

Note that BinSPreader is a part of SPAdes package now, so you can just build it (https://ablab.github.io/spades/binspreader.html)

IanDMedeiros commented 1 month ago

Thanks for the quick response. I installed the binaries from the latest SPAdes release on github yesterday. That is not the latest version of BinSPreader?

asl commented 1 month ago

BinSPreader is a part of source release, but not a part of binary release (it is a separate tool after all). You'd need to build it from source.

IanDMedeiros commented 1 month ago

Ok. Thank you, I will build everything from source. But fyi the (apparently incorrect) BinSPreader binary was present in the SPAdes binary release that I downloaded from Github.

asl commented 1 month ago

But fyi the (apparently incorrect) BinSPreader binary was present in the SPAdes binary release that I downloaded from Github.

Oh, right, sorry, my bad. Then we need to check what is going on, everything should be compatible.

IanDMedeiros commented 1 month ago

Unfortunately compiling BinSPreader from the source code has completely defeated me. The main SPAdes modules all compile, but no matter what I try* the compilation still has "binspreader project is disabled"

I noticed that the instructions at https://ablab.github.io/spades/binspreader.html still reference GFA 1.0 format; is that page outdated?

*Attempted following the instructions at https://ablab.github.io/spades/installation.html: SPADES_ENABLE_PROJECTS="binspreader" ./spades_compile.sh SPADES_ENABLE_PROJECTS="all" ./spades_compile.sh ./spades_compile.sh SPADES_ENABLE_PROJECTS="all" ./spades_compile.sh -SPADES_ENABLE_PROJECTS="all" ./spades_compile.sh SPADES_ENABLE_PROJECTS="binspreader" ./spades_compile.sh -SPADES_ENABLE_PROJECTS="binspreader"

EDITED: Never mind, I see now that it is DSPADES_ENABLE_PROJECT not SPADES_ENABLE_PROJECT. That seems to have worked.

asl commented 1 month ago

EDITED: Never mind, I see now that it is DSPADES_ENABLE_PROJECT not SPADES_ENABLE_PROJECT. That seems to have worked.

Yes, it is -DSPADES_ENABLE_PROJECTS="all". Looks like the line break might happen in unfortunate place, but we cannot limit this :(

IanDMedeiros commented 1 week ago

Hi @asl - Did you have a chance to check whether there is a problem with the BinSPreader binary packaged with the SPAdes 4.0 release for linux? Unfortunately I have not been able to successfully compile BinSPreader on our HPC.