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finished abnormally, OS return value: -11 and source code intasll error #1249
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Hello
If you'd scale your job down to 8 or 16 threads, does it help? |
And for this particular issue we'd need a complete make log |
Hi asl, Here another issue I wanna consult with you. I have two dataset stopped at read error correction stage for over a week. Thanks for your time. |
As usual – there is no telepathy module embedded in SPAdes. So, please do provide spades.log file :) |
Hi asl, Here is the spades.log stopped in read error correction stage. Thanks. |
Does run it with source code installation version gonna help? |
Hi asl, My spades is still in read error correction stage with source code installation version. Waiting for your advice. Thanks. |
Hello, |
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
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