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xHLA: Fast and accurate HLA typing from short read sequence data
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Error: Error detecting input file format. First line seems to be blank. #57

Open AlisaFbb opened 4 years ago

AlisaFbb commented 4 years ago

I try to run xHLA on bam-file (size 11,1 GB) and get an error: Error: Error detecting input file format. First line seems to be blank.

But the first line is not empty. This is a top of header for sam-file derived from the bam-file:

@HD     VN:1.4  SO:coordinate
@SQ     SN:chr1 LN:248956422
@SQ     SN:chr2 LN:242193529
@SQ     SN:chr3 LN:198295559
@SQ     SN:chr4 LN:190214555
@SQ     SN:chr5 LN:181538259
@SQ     SN:chr6 LN:170805979
@SQ     SN:chr7 LN:159345973
@SQ     SN:chr8 LN:145138636
@SQ     SN:chr9 LN:138394717
@SQ     SN:chr10        LN:133797422
@SQ     SN:chr11        LN:135086622
@SQ     SN:chr12        LN:133275309
@SQ     SN:chr13        LN:114364328
@SQ     SN:chr14        LN:107043718
@SQ     SN:chr15        LN:101991189
@SQ     SN:chr16        LN:90338345
@SQ     SN:chr17        LN:83257441
@SQ     SN:chr18        LN:80373285
@SQ     SN:chr19        LN:58617616
@SQ     SN:chr20        LN:64444167
@SQ     SN:chr21        LN:46709983
@SQ     SN:chr22        LN:50818468
@SQ     SN:chrX LN:156040895
@SQ     SN:chrY LN:57227415
@SQ     SN:chrM LN:16569
...

This is a head of the sam-file without header:

A01013:110:HCJ3JDSXY:1:2207:19786:3161  2129    chr1    10732   0       120H30M chr7    102930989       0       GCAGGCGCAGAGAGGCGCGCCGCGCCGGCG  FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF  RG:Z:260003040807_S14   AS:i:30 XS:i:30 NM:i:0  SA:Z:chr7,102931085,-,125M25S,250,1;
A01013:110:HCJ3JDSXY:2:2141:6497:26960  2145    chr1    16194   0       30M121H chr6    78818173        0       GAGCTGGACCCCTGAGCTAGCCATGCTCTG  :F:FFFFF:FFFFFF:FFFFFFFFFFFFFF  RG:Z:260003040807_S14   AS:i:30 XS:i:30 NM:i:0  SA:Z:chr6,78818060,+,25S126M,144,0;
A01013:110:HCJ3JDSXY:3:1608:21540:29841 2113    chr1    19477   0       30M121H =       190561119       190541714       CTCTAAAGGTTGGAATGAATGGCCTAGAAT  FFFFFFFFFFF:FFFFFFFFFFFFFFFFFF  RG:Z:260003040807_S14   AS:i:30 XS:i:30 NM:i:0  SA:Z:chr1,190561316,-,126M25S,250,0;
A01013:110:HCJ3JDSXY:4:1307:1425:12978  2113    chr1    22089   0       30M121H chr16   79884662        0       GTGTGTCATAGTCCCCTGGCCCCATTAATG  FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF  RG:Z:260003040807_S14   AS:i:30 XS:i:30 NM:i:0  SA:Z:chr16,79885035,-,126M25S,250,0;
A01013:110:HCJ3JDSXY:4:2233:22119:28463 2113    chr1    25704   0       30M121H chr12   105982062       0       CCTATAAATAGGCCTAATCACAGCCCCTCA  FFFFFF:FFFFFFFFFFFFFFFFFF::FF,  RG:Z:260003040807_S14   AS:i:30 XS:i:30 NM:i:0  SA:Z:chr12,105982337,-,8S118M25S,218,5;
A01013:110:HCJ3JDSXY:2:2270:9236:13291  2129    chr1    27785   0       119H30M chr3    106467444       0       ACTGCTAATAATACCTACACATGTTAGAAC  FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF  RG:Z:260003040807_S14   AS:i:30 XS:i:30 NM:i:0  SA:Z:chr3,106467679,-,124M25S,212,5;
A01013:110:HCJ3JDSXY:2:1547:13494:22200 2129    chr1    30776   0       121H30M =       217933355       217902651       CCTTTGGTAGGTAATTACGGTTAGATGAGG  FF,FFFFFFFFFFFFFF:,FFFFFFFFFFF  RG:Z:260003040807_S14   AS:i:30 XS:i:30 NM:i:0  SA:Z:chr1,217933407,-,126M25S,110,5;
A01013:110:HCJ3JDSXY:4:1640:26422:3411  2129    chr1    31308   0       121H30M chr2    35378125        0       TCTTTGTGTGACCCTGGGCAAGCCATGAAT  FF::FFFFFFFFFFFFFFFFFFFFFFFFFF  RG:Z:260003040807_S14   AS:i:30 XS:i:30 NM:i:0  SA:Z:chr2,35378293,-,126M25S,250,0;
A01013:110:HCJ3JDSXY:4:2146:5177:30906  2129    chr1    33596   0       121H30M chr18   3222972 0       ATGCGTGTGCCATGTTGGTTTGCTGCACCC  F,FF:FFFFFFFFFFFFFFFFFFFFFFFFF  RG:Z:260003040807_S14   AS:i:30 XS:i:30 NM:i:0  SA:Z:chr18,3223230,-,126M25S,198,5;

How does xHLA process my file? Why does xHLA take the first line as empty, although it is not? Can you help me with this problem?