Quasimapping fails with an instance of 'std::out_of_range'

[iqbal-lab]

Tried quasimapping 100k human reads to the 1000g-5percent PRG:

2018-01-27 20:36:44,322 gramtools    INFO     Start process: quasimap
2018-01-27 20:36:44,441 gramtools    INFO     stdout:

2018-01-27 23:40:22,681 gramtools    INFO     Process termination message:
terminate called after throwing an instance of 'std::out_of_range'
  what():  stoi

2018-01-27 23:40:22,682 gramtools    INFO     Process termination code: -6
2018-01-27 23:40:22,682 gramtools    ERROR    Error code != 0
2018-01-27 23:40:22,682 gramtools    INFO     Output run directory:
gram-5perc/quasimap_outputs/1517085404_ksize15
2018-01-27 23:45:57,164 gramtools    INFO     End process: quasimap
Executing quasimap command
Loading data

Results json:

{
    "start_time": "1517085404",
    "end_time": "1517096757",
    "total_runtime": 11353,
    "gramtools_cpp_quasimap": {
        "command": "/Net/fs1/home/zam/dev/git/gramtools_virtualenv/lib/python3.5/site-packages/gramtools/bin/gram quasimap --gram gram-5perc/ --reads NA12878.100k_reads.fq --kmer-size 1
5 --run-directory gram-5perc/quasimap_outputs/1517085404_ksize15",
        "return_value_is_0": false,
        "stdout": [
            "Executing quasimap command",
            "Loading data"
        ]
    },
    "current_working_directory": "/data2/users/zam/analyses/2018/0122_test_gramtools_on_human",
    "paths": {
        "perl_generated_vcf": "gram-5perc/perl_generated_vcf",
        "kmer_index": "gram-5perc/kmers/kmer_index_15",
        "vcf": "",
        "project": "gram-5perc/",
        "quasimap_run_dirpath": "gram-5perc/quasimap_outputs/1517085404_ksize15",
        "encoded_prg": "gram-5perc/encoded_prg",
        "perl_generated_fa": "gram-5perc/perl_generated_fa",
        "prg": "gram-5perc/prg",
        "variant_site_mask": "gram-5perc/variant_site_mask",
        "allele_mask": "gram-5perc/allele_mask",
        "reference": "",
        "reads": "NA12878.100k_reads.fq",
        "fm_index": "gram-5perc/fm_index",
        "run_report": "gram-5perc/quasimap_outputs/1517085404_ksize15/report.json",
        "quasimap_outputs_dirpath": "gram-5perc/quasimap_outputs"
    },
    "path_hashes": {
        "perl_generated_vcf": "646a637ac640438512783e732e9980dacbe37cb2a24cfe8761d68611eae2ae10",
        "variant_site_mask": "946f8345bbfce0f92a30e40c4d957746bc639942a8cb815454456e7a2a570b3d",
        "reads": "679ee3a253aad81eb4d3e01339842388c4e00d3f338b63f984a3ff7013f54eef",
        "allele_mask": "99a027720bd07cc8b1111e2abd167111c014fe7cc77dad5e0804eddae7ea712e",
        "fm_index": "c007ac4ace24d9430e89f260aa80bc40628984a5d86ef0753788ddd18519309e",
        "encoded_prg": "512689dde7ae6dec180af99dbdab6458ff6d21808c8b05c7432707689bffc3fc",
        "perl_generated_fa": "3c8c4e516a5583ab43556f6c8cfd8fafa42354a80306992ec4d577793074baa0",
        "prg": "026bff525f539356d9beb8ce37814c165346b4618fe014e947f20fc9ea687434"
    },
    "version_report": {
        "version_number": "0.5.0",
        "last_git_commit_hash": "7a53428da84d096805ee51679b60d376cc588cb2",
        "current_git_branch": "master",
        "truncated_git_commits": [
            "7a53428 - Robyn Ffrancon, 4 minutes ago : disable unit tests which depend on unstable ordered data structure",
            "31d8c13 - Robyn Ffrancon, 20 minutes ago : remove biopython dependancy",
            "be2838b - Robyn Ffrancon, 3 hours ago : updated install instructions given new python3 functionality",
            "addd790 - Robyn Ffrancon, 4 hours ago : added instructions for installing without root",
            "26094ea - Robyn Ffrancon, 21 hours ago : fix: gram executable called from gramtools python module with correct enviroment variables for finding libraries"
        ]
    }
}

[iqbal-lab]

wow, took two hours to crash, and hadn't mapped any reads

[iqbal-lab]

I'd scp all the files over to EBI so we can reproduce locally.

[ffranr]

This shouldn't occur any more now that the kmer index is serialized. stoi is not called.

This commit will ensure that the serialized kmer bases are valid: https://github.com/iqbal-lab-org/gramtools/commit/549fc5c8dc35335840fa08f0deb9e34991a72f02

[iqbal-lab]

Any chance you could rerun on the same dataset?

[iqbal-lab]

Closing