Closed ever4cyth closed 4 years ago
were the bwa index built with the same version as the one used for alignments? If not, you must re-build the index of the reference HLA sequences with the version of bwa installed on your system. Cheers, Rene
one of the ways is that lower your bwa version to match the HLAminer
According to readme-first in test-demo folder
For HLAminer predictions from short Read Alignments, run: ./HPRArnaseq_classI.sh
Running bwa... [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... ./HPRArnaseq_classI.sh: line 3: 189118 Segmentation fault (core dumped) bwa aln -e 0 -o 0 ../database/HLA_ABC_CDS.fasta rd1.fq > aln_test.1.sai [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... ./HPRArnaseq_classI.sh: line 4: 189120 Segmentation fault (core dumped) bwa aln -e 0 -o 0 ../database/HLA_ABC_CDS.fasta rd2.fq > aln_test.2.sai [fread] Unexpected end of file Predicting HLA...
both v1.3 and v1.3.1 gave the same error. Could you please help? Thanks!