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nanoporetech / ont-assembly-polish

ONT assembly and Illumina polishing pipeline
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samtools problem #3

Closed gaworj closed 7 years ago

gaworj commented 7 years ago

Hello,

we have successfully installed ont-assembly polish pipeline but I find two problems. First is related to samtools command section in "analysis.mk" file:

@echo Aligning Illumina reads using BWA mem. @bwa mem -t $(CORES) $(BWA_PARAMETERS) $(RACON_CONTIGS) $(ILLUMINA_READS_PAIR1) $(ILLUMINA_READS_PAIR2)\ | samtools view -S -b -u - | samtools sort -@ $(CORES) - $(BWA_BAM_PREFIX)

In such case pipeline crashes.. We find that correcting commands this way helps:

@echo Aligning Illumina reads using BWA mem. @bwa mem -t $(CORES) $(BWA_PARAMETERS) $(RACON_CONTIGS) $(ILLUMINA_READS_PAIR1) $(ILLUMINA_READS_PAIR2) | samtools view -S -b -u - | samtools sort - $(BWA_BAM_PREFIX)

Second issue is related to racon installation/working - I find it several days ago: After pipeline start racon shows this message:

/usr/bin/ld: ./bin/racon: undefined reference to symbol 'clock_gettime@@GLIBC_2.2.5' /usr/bin/ld: note: 'clock_gettime@@GLIBC_2.2.5' is defined in DSO /lib64/librt.so.1 so try adding it to the linker command line /lib64/librt.so.1: could not read symbols: Invalid operation collect2: error: ld returned 1 exit status make[1]: [linux] Error 1 make[1]: Leaving directory `/home/data/analysis/janek/E_albertii_5-2/E_albertii_5-2_polish_v1/racon.build' make: [/home/data/analysis/janek/E_albertii_5-2/E_albertii_5-2_polish_v1/racon] Error 2

I found on racon website that new version is available. Maybe that's the case..

Thanks, Jan

bsipos commented 7 years ago

Hello,

Thanks for reporting these issue. I will fix the samtools sort issue ASAP. Regarding the racon issue: please report it to https://github.com/isovic

Regards, Botond Sipos