*** No rule to make target 'modules'. Stop.

[TseWue]

Hi everyone,

I am trying to get the ont-assembly-polish pipeline to run on our server (no docker allowed unfortunately) and when I issue the $make all command I get the following error:

[tswuethrich@submit01 ont-assembly-polish]$ make all (cd ./assembly-polish && git clone https://github.com/isovic/racon.git racon.build && cd racon.build && make modules && make tools && make -j) &&\ mv ./assembly-polish/racon.build/bin/racon ./assembly-polish/ && rm -rf racon.build Cloning into 'racon.build'... remote: Enumerating objects: 1994, done. remote: Total 1994 (delta 0), reused 0 (delta 0), pack-reused 1994 Receiving objects: 100% (1994/1994), 8.92 MiB | 3.17 MiB/s, done. Resolving deltas: 100% (1271/1271), done. make[1]: Entering directory /gpfs/homefs/ifik/tswuethrich/ONT/mock_hybrid_assembly/nanoporetech_pipeline/ont-assembly-polish/assembly-polish/racon.build make[1]: * No rule to make target modules. Stop. make[1]: Leaving directory `/gpfs/homefs/ifik/tswuethrich/ONT/mock_hybrid_assembly/nanoporetech_pipeline/ont-assembly-polish/assembly-polish/racon.build' *make: [assembly-polish/racon] Error 2**

I did a little investigation and (correct me if I'm wrong - I'm just a beginner) I found that the problem somehow occurs in the command of the analysis.mk file on line 36:

[...] build_racon: $(WDIR)/racon $(WDIR)/racon: $(WDT) (cd $(WDIR) && git clone https://github.com/isovic/racon.git racon.build && cd racon.build && make modules && make tools && make -j) &&\ mv $(WDIR)/racon.build/bin/racon $(WDIR)/ && rm -rf racon.build [...]

The racon.build directory is being built with the contents dir vendor dir test dir src dir scripts README.md LICENSE CMakeLists.txt

Do I have to specify any other thing (like modifying another file within this directory?) I already asked our in-house linux geek and he suggested to turn to you for help. :-)

Thanks a bunch and have a nice day! Best, -Tse

[bsipos]

Hello,

The commands for compiling racon were outdated. I have fixed the problem and pushed to GitHub. Please try running your analysis again.

Regards, Botond

[TseWue]

Hi,

Thanks a lot, yes it worked now. However, not entirely, I encounter a segfault at

[...] Mapping nanopore reads onto canu contings using minimap. /bin/sh: line 1: 18914 Segmentation fault minimap ./assembly-polish/canu-assembly/canu.contigs.fasta /gpfs/homefs/ifik/tswuethrich/ONT/mock_hybrid_assembly/ont_reads_mock/all_mock_stringent.fastq > ./assembly-polish/minimap_overlaps.paf make: *** [assembly-polish/racon.contigs.fasta] Error 139 [...]

The _minimapoverlaps.paf is written but it remains empty. The problem persists everytime I rerun the pipeline. My files are not particularly big, do you have an idea what the problem could be?

Thanks for your help. Best, Tse

[bsipos]

Hello,

I have updated the pipeline to work with minimap2 (instead of minimap). Could you please pull and try again?

Regards, Botond