No indicies/hla_backbone.fa file found

[aforsythe]

I'm currently trying to run hisat_genotype in a docker container due to #66

Below is my Dockerfile

FROM biocontainers/biocontainers:vdebian-buster-backports_cv1

USER root
ENV DEBIAN_FRONTEND noninteractive
ENV PATH=/hisatgenotype:/hisatgenotype/hisat2:$PATH
ENV PYTHONPATH=/hisatgenotype/hisatgenotype_modules:$PYTHONPATH

RUN apt-get update && \
    apt-get install -y \
    build-essential \
    git \
    wget \
    libhdf5-dev \
    libcurl4-gnutls-dev \
    libssl-dev \
    libxml2-dev \
    libpng-dev \
    zlib1g-dev \
    samtools \
    python3.7 && \
    apt-get clean && apt-get purge && \
    rm -rf /var/lib/apt/lists/* /tmp/*

RUN ln -sf /usr/bin/python3 /usr/bin/python && \
    ln -sf /usr/bin/pip3 /usr/bin/pip

RUN git clone https://github.com/DaehwanKimLab/hisat-genotype.git /hisatgenotype
WORKDIR /hisatgenotype
RUN ["/bin/bash", "setup.sh", "-r"]

USER biodocker
WORKDIR /data/

The container appears to build correctly as verified using

hisatgenotype --help
hisat2 --help

Per the tutorial, I've downloaded and unziped ILMN.tar.gz to /data using

wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat-genotype/data/hla/ILMN.tar.gz
tar xvzf ILMN.tar.gz

When I run

docker run -it --rm -v ${PWD}:/data hisat-genotype hisatgenotype --base hla --locus-list A -1 ILMN/NA12892.extracted.1.fq.gz -2 ILMN/NA12892.extracted.2.fq.gz

I get

	1: Extracting reads from NA12892.extracted.1.fq.gz
No /hisatgenotype/indicies/hla_backbone.fa file found
Building hla Database

and the container exists. The generated /data/hisatgenotype_out/ directory is empty.

The current contents of /hisatgenotype/indicies are

docker run -it --rm -v ${PWD}:/data hisat-genotype ls -la /hisatgenotype/indicies
total 14701264
drwxr-xr-x 4 root root       4096 Apr 10 19:13 .
drwxr-xr-x 1 root root       4096 Apr 10 18:33 ..
-rw-r--r-- 1 root root 3151425857 Apr 10 19:13 genome.fa
-rw-r--r-- 1 root root       6406 Apr 10 19:13 genome.fa.fai
-rw-r--r-- 1 1041 1008 2061360111 Jan 28  2018 genotype_genome.1.ht2
-rw-r--r-- 1 1041 1008  831734308 Jan 28  2018 genotype_genome.2.ht2
-rw-r--r-- 1 1041 1008      11294 Jan 28  2018 genotype_genome.3.ht2
-rw-r--r-- 1 1041 1008  736464771 Jan 28  2018 genotype_genome.4.ht2
-rw-r--r-- 1 1041 1008 2155012255 Jan 28  2018 genotype_genome.5.ht2
-rw-r--r-- 1 1041 1008  786608148 Jan 28  2018 genotype_genome.6.ht2
-rw-r--r-- 1 1041 1008  510733900 Jan 28  2018 genotype_genome.7.ht2
-rw-r--r-- 1 1041 1008  158859306 Jan 28  2018 genotype_genome.8.ht2
-rw-r--r-- 1 1041 1008     229600 Jan 28  2018 genotype_genome.allele
-rw-r--r-- 1 1041 1008          0 Jan 28  2018 genotype_genome.clnsig
-rw-r--r-- 1 1041 1008       5708 Jan 28  2018 genotype_genome.coord
-rw-r--r-- 1 1041 1008 3151436038 Jan 28  2018 genotype_genome.fa
-rw-r--r-- 1 1041 1008       6406 Jan 28  2018 genotype_genome.fa.fai
-rw-r--r-- 1 1041 1008  581916335 Jan 28  2018 genotype_genome.haplotype
-rw-r--r-- 1 1041 1008  461795109 Jan 28  2018 genotype_genome.index.snp
-rw-r--r-- 1 1041 1008    4275468 Jan 28  2018 genotype_genome.link
-rw-r--r-- 1 1041 1008       4722 Jan 28  2018 genotype_genome.locus
-rw-r--r-- 1 1041 1008     193036 Jan 28  2018 genotype_genome.partial
-rw-r--r-- 1 1041 1008  461902278 Jan 28  2018 genotype_genome.snp
drwxr-sr-x 2 1041 1008       4096 Mar 17  2016 grch38
drwxr-xr-x 6 root root       4096 Apr 10 19:13 hisatgenotype_db

How can I generate hla_backbone.fa and get the typing output?

[aforsythe]

Actually, perhaps everything is not running correctly
Last line of the help indicates (ERR): hisat2-align exited with value 1
Not sure why

Update
Error generated here was user error ... ran hisat2 instead of hisat2 --help
Sorry for the confusion

biodocker@f93ea1484a6a:/data$ hisat2
No index, query, or output file specified!
HISAT2 version 2.2.1 by Daehwan Kim ([email protected], www.ccb.jhu.edu/people/infphilo)
Usage:
  hisat2 [options]* -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]

  <ht2-idx>  Index filename prefix (minus trailing .X.ht2).
  <m1>       Files with #1 mates, paired with files in <m2>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <m2>       Files with #2 mates, paired with files in <m1>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <r>        Files with unpaired reads.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <sam>      File for SAM output (default: stdout)

  <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
  specified many times.  E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

 Input:
  -q                 query input files are FASTQ .fq/.fastq (default)
  --qseq             query input files are in Illumina's qseq format
  -f                 query input files are (multi-)FASTA .fa/.mfa
  -r                 query input files are raw one-sequence-per-line
  -c                 <m1>, <m2>, <r> are sequences themselves, not files
  -s/--skip <int>    skip the first <int> reads/pairs in the input (none)
  -u/--upto <int>    stop after first <int> reads/pairs (no limit)
  -5/--trim5 <int>   trim <int> bases from 5'/left end of reads (0)
  -3/--trim3 <int>   trim <int> bases from 3'/right end of reads (0)
  --phred33          qualities are Phred+33 (default)
  --phred64          qualities are Phred+64
  --int-quals        qualities encoded as space-delimited integers

 Presets:                 Same as:
   --fast                 --no-repeat-index
   --sensitive            --bowtie2-dp 1 -k 30 --score-min L,0,-0.5
   --very-sensitive       --bowtie2-dp 2 -k 50 --score-min L,0,-1

 Alignment:
  --bowtie2-dp <int> use Bowtie2's dynamic programming alignment algorithm (0) - 0: no dynamic programming, 1: conditional dynamic programming, and 2: unconditional dynamic programming (slowest)
  --n-ceil <func>    func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
  --ignore-quals     treat all quality values as 30 on Phred scale (off)
  --nofw             do not align forward (original) version of read (off)
  --norc             do not align reverse-complement version of read (off)
  --no-repeat-index  do not use repeat index

 Spliced Alignment:
  --pen-cansplice <int>              penalty for a canonical splice site (0)
  --pen-noncansplice <int>           penalty for a non-canonical splice site (12)
  --pen-canintronlen <func>          penalty for long introns (G,-8,1) with canonical splice sites
  --pen-noncanintronlen <func>       penalty for long introns (G,-8,1) with noncanonical splice sites
  --min-intronlen <int>              minimum intron length (20)
  --max-intronlen <int>              maximum intron length (500000)
  --known-splicesite-infile <path>   provide a list of known splice sites
  --novel-splicesite-outfile <path>  report a list of splice sites
  --novel-splicesite-infile <path>   provide a list of novel splice sites
  --no-temp-splicesite               disable the use of splice sites found
  --no-spliced-alignment             disable spliced alignment
  --rna-strandness <string>          specify strand-specific information (unstranded)
  --tmo                              reports only those alignments within known transcriptome
  --dta                              reports alignments tailored for transcript assemblers
  --dta-cufflinks                    reports alignments tailored specifically for cufflinks
  --avoid-pseudogene                 tries to avoid aligning reads to pseudogenes (experimental option)
  --no-templatelen-adjustment        disables template length adjustment for RNA-seq reads

 Scoring:
  --mp <int>,<int>   max and min penalties for mismatch; lower qual = lower penalty <6,2>
  --sp <int>,<int>   max and min penalties for soft-clipping; lower qual = lower penalty <2,1>
  --no-softclip      no soft-clipping
  --np <int>         penalty for non-A/C/G/Ts in read/ref (1)
  --rdg <int>,<int>  read gap open, extend penalties (5,3)
  --rfg <int>,<int>  reference gap open, extend penalties (5,3)
  --score-min <func> min acceptable alignment score w/r/t read length
                     (L,0.0,-0.2)

 Reporting:
  -k <int>           It searches for at most <int> distinct, primary alignments for each read. Primary alignments mean
                     alignments whose alignment score is equal to or higher than any other alignments. The search terminates
                     when it cannot find more distinct valid alignments, or when it finds <int>, whichever happens first.
                     The alignment score for a paired-end alignment equals the sum of the alignment scores of
                     the individual mates. Each reported read or pair alignment beyond the first has the SAM ‘secondary’ bit
                     (which equals 256) set in its FLAGS field. For reads that have more than <int> distinct,
                     valid alignments, hisat2 does not guarantee that the <int> alignments reported are the best possible
                     in terms of alignment score. Default: 5 (linear index) or 10 (graph index).
                     Note: HISAT2 is not designed with large values for -k in mind, and when aligning reads to long,
                     repetitive genomes, large -k could make alignment much slower.
  --max-seeds <int>  HISAT2, like other aligners, uses seed-and-extend approaches. HISAT2 tries to extend seeds to
                     full-length alignments. In HISAT2, --max-seeds is used to control the maximum number of seeds that
                     will be extended. For DNA-read alignment (--no-spliced-alignment), HISAT2 extends up to these many seeds
                     and skips the rest of the seeds. For RNA-read alignment, HISAT2 skips extending seeds and reports
                     no alignments if the number of seeds is larger than the number specified with the option,
                     to be compatible with previous versions of HISAT2. Large values for --max-seeds may improve alignment
                     sensitivity, but HISAT2 is not designed with large values for --max-seeds in mind, and when aligning
                     reads to long, repetitive genomes, large --max-seeds could make alignment much slower.
                     The default value is the maximum of 5 and the value that comes with -k times 2.
  -a/--all           HISAT2 reports all alignments it can find. Using the option is equivalent to using both --max-seeds
                     and -k with the maximum value that a 64-bit signed integer can represent (9,223,372,036,854,775,807).
  --repeat           report alignments to repeat sequences directly

 Paired-end:
  -I/--minins <int>  minimum fragment length (0), only valid with --no-spliced-alignment
  -X/--maxins <int>  maximum fragment length (500), only valid with --no-spliced-alignment
  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
  --no-mixed         suppress unpaired alignments for paired reads
  --no-discordant    suppress discordant alignments for paired reads

 Output:
  -t/--time          print wall-clock time taken by search phases
  --un <path>           write unpaired reads that didn't align to <path>
  --al <path>           write unpaired reads that aligned at least once to <path>
  --un-conc <path>      write pairs that didn't align concordantly to <path>
  --al-conc <path>      write pairs that aligned concordantly at least once to <path>
  (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
  --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
  --summary-file <path> print alignment summary to this file.
  --new-summary         print alignment summary in a new style, which is more machine-friendly.
  --quiet               print nothing to stderr except serious errors
  --met-file <path>     send metrics to file at <path> (off)
  --met-stderr          send metrics to stderr (off)
  --met <int>           report internal counters & metrics every <int> secs (1)
  --no-head             suppress header lines, i.e. lines starting with @
  --no-sq               suppress @SQ header lines
  --rg-id <text>        set read group id, reflected in @RG line and RG:Z: opt field
  --rg <text>           add <text> ("lab:value") to @RG line of SAM header.
                        Note: @RG line only printed when --rg-id is set.
  --omit-sec-seq        put '*' in SEQ and QUAL fields for secondary alignments.

 Performance:
  -o/--offrate <int> override offrate of index; must be >= index's offrate
  -p/--threads <int> number of alignment threads to launch (1)
  --reorder          force SAM output order to match order of input reads
  --mm               use memory-mapped I/O for index; many 'hisat2's can share

 Other:
  --qc-filter        filter out reads that are bad according to QSEQ filter
  --seed <int>       seed for random number generator (0)
  --non-deterministic seed rand. gen. arbitrarily instead of using read attributes
  --remove-chrname   remove 'chr' from reference names in alignment
  --add-chrname      add 'chr' to reference names in alignment
  --version          print version information and quit
  -h/--help          print this usage message
(ERR): hisat2-align exited with value 1

[aforsythe]

This particular issue seems to be related to the base docker image I was using. Changing to FROM ubuntu:18.04 seems to solve the no indicies/hla_backbone.fa problem