make -C submodules/Flye error

[Penny2023James]

Hi I faced an error when I tried to make submodules/Flye

######################################################### z5438778@k250:~/stRainy $ make -C submodules/Flye make: Entering directory '/home/z5438778/stRainy/submodules/Flye' make -C /home/z5438778/stRainy/submodules/Flye/lib/minimap2 -j 4 make[1]: Entering directory '/home/z5438778/stRainy/submodules/Flye/lib/minimap2' cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC bseq.c -o bseq.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC sketch.c -o sketch.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC sdust.c -o sdust.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC options.c -o options.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC index.c -o index.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC chain.c -o chain.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC align.c -o align.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC hit.c -o hit.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC map.c -o map.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC format.c -o format.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC pe.c -o pe.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC esterr.c -o esterr.o cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC splitidx.c -o splitidx.o cc -c -g -Wall -O2 -Wc++-compat -msse2 -DHAVE_KALLOC ksw2_ll_sse.c -o ksw2_ll_sse.o cc -c -g -Wall -O2 -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extz2_sse.c -o ksw2_extz2_sse41.o cc -c -g -Wall -O2 -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extd2_sse.c -o ksw2_extd2_sse41.o cc -c -g -Wall -O2 -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_exts2_sse.c -o ksw2_exts2_sse41.o cc -c -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extz2_sse.c -o ksw2_extz2_sse2.o cc -c -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extd2_sse.c -o ksw2_extd2_sse2.o cc -c -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_exts2_sse.c -o ksw2_exts2_sse2.o cc -c -g -Wall -O2 -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_dispatch.c -o ksw2_dispatch.o ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o cc -g -Wall -O2 -Wc++-compat main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread /bin/ld: main.o: unable to initialize decompress status for section .debug_info /bin/ld: main.o: unable to initialize decompress status for section .debug_info /bin/ld: main.o: unable to initialize decompress status for section .debug_info /bin/ld: main.o: unable to initialize decompress status for section .debug_info main.o: file not recognized: File format not recognized collect2: error: ld returned 1 exit status make[1]: [Makefile:46: minimap2] Error 1 make[1]: Leaving directory '/home/z5438778/stRainy/submodules/Flye/lib/minimap2' make: [Makefile:25: /home/z5438778/stRainy/submodules/Flye/bin/flye-minimap2] Error 2 make: Leaving directory '/home/z5438778/stRainy/submodules/Flye' ############################################################################ Does anyone know how to solve this? Any suggestions are welcome Thank you

[mikolmogorov]

Hello,

This error may be caused by inconsistencies in your developer libraries. Are you using conda environment for building? I'd suggest trying to disable it and build with only system libraries. If that doesn't help, please provide more info about your system, and also gcc --version / cc --version

[Penny2023James]

Hi, Thank you for the quick response, I tried building it in a conda environment and without but both of them shows error. Below is the error that showed when I build without conda env ############################################################################ z5438778@k143:~/stRainy $ make -C submodules/Flye make: Entering directory '/home/z5438778/stRainy/submodules/Flye' make -C /home/z5438778/stRainy/submodules/Flye/lib/minimap2 -j 4 make[1]: Entering directory '/home/z5438778/stRainy/submodules/Flye/lib/minimap2' cc -g -Wall -O2 -Wc++-compat main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread /bin/ld: main.o: unable to initialize decompress status for section .debug_info /bin/ld: main.o: unable to initialize decompress status for section .debug_info /bin/ld: main.o: unable to initialize decompress status for section .debug_info /bin/ld: main.o: unable to initialize decompress status for section .debug_info main.o: file not recognized: File format not recognized collect2: error: ld returned 1 exit status make[1]: [Makefile:46: minimap2] Error 1 make[1]: Leaving directory '/home/z5438778/stRainy/submodules/Flye/lib/minimap2' make: [Makefile:25: /home/z5438778/stRainy/submodules/Flye/bin/flye-minimap2] Error 2 make: Leaving directory '/home/z5438778/stRainy/submodules/Flye' ############################################################################ I am now using Linux k143 4.18.0-477.15.1.el8_8.x86_64, with gcc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-18)/ cc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-18)

[mikolmogorov]

Strange, something must be inconsistent in your developer environment / packages. The building error is in fact in the minimap2, so we don't have much control over that. Are you able to build other biolinformatics tools from source on this system?

[mikolmogorov]

Closed due to inactivity, feel free to reopen if the issue remains!