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humanlongevity / HLA

xHLA: Fast and accurate HLA typing from short read sequence data
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xHLA invalid input file, /get-reads-alt-unmap.sh not working. #37

Open gunyorka opened 5 years ago

gunyorka commented 5 years ago

Dear Authors!

I'm dealing with the next problem, using xHLA:

In our research we are trying to carry out HLA genotyping on exome sequencing data of asthmatic patients. The .SRA files we downloaded are aligned to GRCH37.

So far we tried to convert our files to hg38 with crossmap

and also manually with samtools, using the following commands: 1.samtools bam2fq SAMPLE.bam > SAMPLE.fastq

  1. cat SAMPLE.fastq | grep '^@./1$' -A 3 --no-group-separator > SAMPLE_r1.fastq cat SAMPLE.fastq | grep '^@./2$' -A 3 --no-group-separator > SAMPLE_r2.fastq
  2. bwa mem "ref.genome_hg_38" sample_r1.fastq sample_r2.fastq
  3. samtools sort sample.bam sample.sorted.bam
  4. samtools index sample.sorted.bam And the input file for xHLA was "sample.sorted.bam"

Each way we got the following error massage from xHLA:

processing FASTQ file found 0 reads processing MSA file found 26381 HLA exons processing FASTQ file Error: Invalid input file format matched to 0 HLA exons 0 reads matched to HLA types not in the MSA file

We also tried the recommenden pre-processing You mention in GitHub, but we were unable to run it from docker, running it manually resulted in the following error: "./get-reads-alt-unmap.sh: line 37: sambamba: command not found ./get-reads-alt-unmap.sh: line 40: sambamba: command not found"

We would highly appreciate your help, Thank you in advance.

tmhmxg59 commented 5 years ago

Did you read 35? I think it might help.

abhisheknrl commented 5 years ago

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yubau1112 commented 5 years ago

Hi you need to install sambamba http://lomereiter.github.io/sambamba/

if still not found sambamba command you can edit get-reads-alt-unmap.sh add absolute path before sambamba command

milkcookie commented 1 year ago

Dear Authors!

I'm dealing with the next problem, using xHLA:

In our research we are trying to carry out HLA genotyping on exome sequencing data of asthmatic patients. The .SRA files we downloaded are aligned to GRCH37.

So far we tried to convert our files to hg38 with crossmap

and also manually with samtools, using the following commands: 1.samtools bam2fq SAMPLE.bam > SAMPLE.fastq 2. cat SAMPLE.fastq | grep '^@._/1$' -A 3 --no-group-separator > SAMPLEr1.fastq cat SAMPLE.fastq | grep '^@./2$' -A 3 --no-group-separator > SAMPLE_r2.fastq 3. bwa mem "ref.genome_hg_38" sample_r1.fastq sample_r2.fastq 4. samtools sort sample.bam sample.sorted.bam 5. samtools index sample.sorted.bam And the input file for xHLA was "sample.sorted.bam"

Each way we got the following error massage from xHLA:

processing FASTQ file found 0 reads processing MSA file found 26381 HLA exons processing FASTQ file Error: Invalid input file format matched to 0 HLA exons 0 reads matched to HLA types not in the MSA file

We also tried the recommenden pre-processing You mention in GitHub, but we were unable to run it from docker, running it manually resulted in the following error: "./get-reads-alt-unmap.sh: line 37: sambamba: command not found ./get-reads-alt-unmap.sh: line 40: sambamba: command not found"

We would highly appreciate your help, Thank you in advance.

Does it work for hg19? @tmhmxg59 @tanghaibao