HISAT2 HLA genotyping errors

Question

[jgibbs]

Hi,
I'm trying to follow the tutorial for HLA typing and assembly in HISAT2 as described at http://ccb.jhu.edu/hisat-genotype/index.php/Type:HLA using my own RNAseq data. I do everything as described. I have samtools 1.7 installed. I am able to extract my HLA reads. But when I get to the last step, the typing and assembly, I get an error "no such file or directory". There seems to be a bam file missing. There is a newly created one in my directory called "-o.bam" but none with the specific name requested.

Any help would be greatly appreciated. Thanks.

with high verbose level and many similar lines deleted for brevity:

[ ~/devel/hisat-genotype-top/hla-analysis ]$  hisatgenotype_locus.py --base hla --locus-list A --verbose-level=5 -1 HLAreads/AB3033-L1_HLVK3BGX3_S1_R1_001.hla.extracted.1.fq.gz -2 HLAreads/AB3033-L1_HLVK3BGX3_S1_R1_001.hla.extracted.2.fq.gz 
    A
        hisat2 graph
hisat2 --mm --no-unal --no-spliced-alignment -X 1000 --max-altstried 64 --haplotype -x hla.graph -p 1 -1 HLAreads/AB3033-L1_HLVK3BGX3_S1_R1_001.hla.extracted.1.fq.gz -2 HLAreads/AB3033-L1_HLVK3BGX3_S1_R1_001.hla.extracted.2.fq.gz
open: No such file or directory
[bam_index_build2] fail to open the BAM file.
number of left haplotypes: 140
    1231-hv5174-1234: set(['1234-hv5177-1234'])
    344-hv4104-346: set(['299-hv4094-346'])
    1537-hv5352-1541: set(['1538-1541'])
    1937-1943: set(['1936-hv5408-1943'])
...
    2128-hv5535-2211: set(['2139-hv5542-2211'])
    679-hv4502-680: set(['677-hv4501-680'])
    306-hv4098-306: set(['300-hv4085-306'])
    1937-hv5407-1943: set(['1936-hv5404-hv5408-1943'])
number of right haplotypes: 119
    2211-hv5593-2213: set(['2211-hv5595-2212'])
    532-hv4190-hv4194-533: set(['532-hv4192-536'])
    1178-hv5059-1179: set(['1178-hv5058-1178'])
    531-hv4188-hv4190-532: set(['531-hv4189-534'])
...
    3254-hv5726-3260: set(['3254-3259'])
    1301-hv5301-1301: set(['1301-hv5303-1302'])
    670-hv4476-671: set(['670-hv4478-672'])
    1250-hv5207-hv5209-hv5216-1254: set(['1250-hv5205-hv5209-hv5216-1253'])
rm: AB3033-L1_HLVK3BGX3_S1_R1_001.hla.bam*: No such file or directory
[ ~/devel/hisat-genotype-top/hla-analysis ]$ 

Answer 1

[jgibbs]

Thanks to all who viewed this post. I solved the problem. Parts of samtools were missing. The problem was that after I made samtools, I put samtools into a directory in $PATH. But I didn't know there were other executables that should have gone there as well, hence they got built but weren't in my $PATH.

Answer 2

[okaMavuso]

Greetings, I seem not able to get past the installation phase $ git clone https://github.com/infphilo/hisat2 hisat-genotype-top getting the following error

fatal: unable to access 'https://github.com/infphilo/hisat2/': Peer reports incompatible or unsupported protocol version. any pointers?

[Charles Warden]

I am currently looking into troubleshooting a downstream step. I also needed to modify an installation file (at least for my system).

However, for the step that you are describing, I could follow the instructions on this page in that I could successfully run the command git clone https://github.com/DaehwanKimLab/hisat-genotype.git

Also, I am not sure if creating a new post may help with receiving responses.