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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.
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?
The text was updated successfully, but these errors were encountered:
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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:
This is a head of the sam-file without header:
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?
The text was updated successfully, but these errors were encountered: