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ecoPCR error #4

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opened 2018-04-16 07:04:29 +00:00 by gui.sempere · 0 comments
gui.sempere commented 2018-04-16 07:04:29 +00:00 (Migrated from git.metabarcoding.org)
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I am trying to design primers from SILVA reference files, using ecoPCR and ecoprimers. The first part of my script consists in the following, that applies to a SILVA fasta preliminarily annotated with NCBI taxids:

ecoPCR/tools/ecoPCRFormat.py --fasta --name ${FASTA_WITH_NCBI_TAX} --taxonomy taxdmp ${FASTA_WITH_NCBI_TAX}.fasta

ecoPCR/src/ecoPCR -d ${FASTA_WITH_NCBI_TAX} -e 2 -D 100 GTGTGCCAGCMGCCGCGGTAA CCGGACTACHVGGGTWTCTAAT > ${FASTA_WITH_NCBI_TAX}_e2_D100_V4.ecoPCR

The second command runs fine when applied to the full SILVA reference file (SILVA_132_SSURef_tax_silva.fasta), however when applied to the NR99 version of this file (SILVA_132_SSURef_Nr99_tax_silva.fasta) it produces the following error:

Reading 1734542 taxa...
No local taxon

Reading file SILVA_132_SSURef_Nr99_tax_ncbi_001.sdx containing 695164 sequences...

*** glibc detected *** ecoPCR/src/ecoPCR: free(): invalid next size (normal): 0x00000000068627d0 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3b86275e66]
/lib64/libc.so.6[0x3b862789b3]
/lib64/libc.so.6[0x3b8627b72e]
/lib64/libc.so.6(realloc+0xe5)[0x3b8627baf5]
ecoPCR/src/ecoPCR[0x4036b8]
ecoPCR/src/ecoPCR[0x4049f4]
ecoPCR/src/ecoPCR[0x403a56]
ecoPCR/src/ecoPCR[0x403c3e]
ecoPCR/src/ecoPCR[0x4029d4]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3b8621ed5d]
ecoPCR/src/ecoPCR[0x400f79]

Any ideas why?

I am trying to design primers from SILVA reference files, using ecoPCR and ecoprimers. The first part of my script consists in the following, that applies to a SILVA fasta preliminarily annotated with NCBI taxids: ecoPCR/tools/ecoPCRFormat.py --fasta --name ${FASTA_WITH_NCBI_TAX} --taxonomy taxdmp ${FASTA_WITH_NCBI_TAX}.fasta ecoPCR/src/ecoPCR -d ${FASTA_WITH_NCBI_TAX} -e 2 -D 100 GTGTGCCAGCMGCCGCGGTAA CCGGACTACHVGGGTWTCTAAT > ${FASTA_WITH_NCBI_TAX}_e2_D100_V4.ecoPCR The second command runs fine when applied to the full SILVA reference file (SILVA_132_SSURef_tax_silva.fasta), however when applied to the NR99 version of this file (SILVA_132_SSURef_Nr99_tax_silva.fasta) it produces the following error: Reading 1734542 taxa... No local taxon # Reading file SILVA_132_SSURef_Nr99_tax_ncbi_001.sdx containing 695164 sequences... *** glibc detected *** ecoPCR/src/ecoPCR: free(): invalid next size (normal): 0x00000000068627d0 *** ======= Backtrace: ========= /lib64/libc.so.6[0x3b86275e66] /lib64/libc.so.6[0x3b862789b3] /lib64/libc.so.6[0x3b8627b72e] /lib64/libc.so.6(realloc+0xe5)[0x3b8627baf5] ecoPCR/src/ecoPCR[0x4036b8] ecoPCR/src/ecoPCR[0x4049f4] ecoPCR/src/ecoPCR[0x403a56] ecoPCR/src/ecoPCR[0x403c3e] ecoPCR/src/ecoPCR[0x4029d4] /lib64/libc.so.6(__libc_start_main+0xfd)[0x3b8621ed5d] ecoPCR/src/ecoPCR[0x400f79] Any ideas why?
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Reference: obitools/ecopcr#4
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