freebayes-parallel

[TheSky222]

my command: snippy --outdir test/mysnps --ref test/REF_GCF_904425475.1_MG1655_genomic\(1\).fna --ctgs test/11657_5\#1.fa"

freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf

dyld: Symbol not found: __ZNKSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE13find_first_ofEPKcmm Referenced from: /usr/local/bin/vcfuniq Expected in: /usr/lib/libstdc++.6.dylib in /usr/local/bin/vcfuniq dyld: Symbol not found: __ZNKSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE13find_first_ofEPKcmm Referenced from: /usr/local/bin/vcfstreamsort Expected in: /usr/lib/libstdc++.6.dylib in /usr/local/bin/vcfstreamsort Traceback (most recent call last): File "/usr/local/bin/vcffirstheader", line 16, in print(line.strip()) BrokenPipeError: [Errno 32] Broken pipe Exception ignored in: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> BrokenPipeError: [Errno 32] Broken pipe /usr/local/bin/freebayes-parallel: line 40: 37224 Exit 141 ( cat "$regionsfile" | parallel -k -j "$ncpus" "${command[@]}" --region {} ) 37225 Exit 120 | vcffirstheader 37226 Abort trap: 6 | vcfstreamsort -w 1000 37228 Abort trap: 6 | vcfuniq

[hafizmtalha]

did you find any solution to this ??