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bcgsc / HLAminer

⛏ HLA predictions from NGS shotgun data
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core dumped #1

Closed ever4cyth closed 4 years ago

ever4cyth commented 6 years ago

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!

warrenlr commented 6 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

nyzhoulang commented 5 years ago

one of the ways is that lower your bwa version to match the HLAminer