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 ]$
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.