finished abnormally, OS return value: -11 and source code intasll error

[2110537]

Description of bug

Dear Spades Team,,

Thanks for your spades.

I encountered an error when using spades: finished abnormally, OS return value: -11.
I used defult paremters and spades spent a long time on read corraction stage. So I added --only-assembler flag. Then I got the error: finished abnormally, OS return value: -11.
Spades.log is attached.

Spades installed by binaries.
After checking other user's and your suggestions, I try to install spades manually, but I got another installtion error:

make[2]: 离开目录“/home/kxy/SPAdes-3.15.5/build_spades”
make[1]: *** [CMakeFiles/Makefile2:2221：common/utils/CMakeFiles/utils.dir/all] 错误 2
[ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o
[ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o
[ 61%] Linking CXX static library libmapping_printer.a
make[2]: 离开目录“/home/kxy/SPAdes-3.15.5/build_spades”
[ 61%] Built target mapping_printer
[ 61%] Linking C static library libhmmer.a
make[2]: 离开目录“/home/kxy/SPAdes-3.15.5/build_spades”
[ 61%] Built target hmmer
make[1]: 离开目录“/home/kxy/SPAdes-3.15.5/build_spades”
make: *** [Makefile:163：all] 错误 2

Could you please give me some intruction on how to install spades manually or on how can I fix the "finished abnormally, OS return value: -11" error.

Thanks!

spades.log

spades.log

params.txt

./metaspades.py -1 /media/data/kxy/coassembly/co-c5-12/co-c5-12_1.fastq -2 /media/data/kxy/coassembly/co-c5-12/co-c5-12_2.fastq -o /media/data/kxy/coassembly/co-c5-12 -t 50 -m 1000 --only-assembler

SPAdes version

spades v3.15.5

Operating System

22.04.1-Ubuntu

Python Version

No response

Method of SPAdes installation

binaries

No errors reported in spades.log

• Yes

[asl]

Hello

0:07:18.411 2M / 1118M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 500 files using 50 threads. This might take a while.

If you'd scale your job down to 8 or 16 threads, does it help?

[asl]

make[2]: 离开目录“/home/kxy/SPAdes-3.15.5/build_spades”
make[1]: *** [CMakeFiles/Makefile2:2221：common/utils/CMakeFiles/utils.dir/all] 错误 2
[ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o
[ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o
[ 61%] Linking CXX static library libmapping_printer.a
make[2]: 离开目录“/home/kxy/SPAdes-3.15.5/build_spades”
[ 61%] Built target mapping_printer
[ 61%] Linking C static library libhmmer.a
make[2]: 离开目录“/home/kxy/SPAdes-3.15.5/build_spades”
[ 61%] Built target hmmer
make[1]: 离开目录“/home/kxy/SPAdes-3.15.5/build_spades”
make: *** [Makefile:163：all] 错误 2

And for this particular issue we'd need a complete make log

[2110537]

Hi asl,
Thanks for your reply.
I found my fatal error: bzlib.h: No such file or directory during run make command. I installed necessary plugins.
Now Spades successfully installed and the dataset was completed successfully.

Here another issue I wanna consult with you. I have two dataset stopped at read error correction stage for over a week.
I'd like to know if the sutiation is normal, is there possible seeing Spades compelete it or should I run Spades with --only-assembler flag. And I see cpus assigned to Spades were totally used.

Thanks for your time.

[asl]

I'd like to know if the sutiation is normal, is there possible seeing Spades compelete it or should I run Spades with --only-assembler flag. And I see cpus assigned to Spades were totally used.

As usual – there is no telepathy module embedded in SPAdes. So, please do provide spades.log file :)

[2110537]

Hi asl,

Here is the spades.log stopped in read error correction stage.
spades.log

Thanks.

[2110537]

Does run it with source code installation version gonna help?

[2110537]

Hi asl,

My spades is still in read error correction stage with source code installation version.
I have no idea what to do.

Waiting for your advice. Thanks.

[Tin-26]

Hello,
I have the same issue with both the Linux version and the source code version.