Simulating higher read depth leads to a KeyError: 'x'

[zoey-rw]

Hi, I'm encountering an error when I change my simulated read depth from 5M to 10M. I'm using an abundance file for 200 draft genomes. This is on a computing cluster with at least 448 GB of RAM available. Environment details are below - any ideas on what's going wrong?

# Works fine for lower read depths
readdepth=10M
# Draft genomes are passed as a list of file paths
file_list=$(cat ./mc_input_fungprop_10_unzipped.txt)


(insilicoseq)[zrwerbin@scc-up2 01_mock_community_input]$ iss generate --draft $file_list --model hiseq --output $out_simulated_reads_path --cpus
 4 --abundance uniform --n_reads $readdepth

INFO:iss.app:Starting iss generate
INFO:iss.generator:Using kde ErrorModel
INFO:iss.util:Stitching input files together
INFO:iss.generator:Using uniform abundance distribution
INFO:iss.app:Using 4 cpus for read generation
INFO:iss.app:Generating 10000000 reads

multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/projectnb/talbot-lab-data/zrwerbin/.conda/envs/insilicoseq/lib/python3.10/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/projectnb/talbot-lab-data/zrwerbin/.conda/envs/insilicoseq/lib/python3.10/multiprocessing/pool.py", line 51, in starmapstar
    return list(itertools.starmap(args[0], args[1]))
  File "/projectnb/talbot-lab-data/zrwerbin/.conda/envs/insilicoseq/lib/python3.10/site-packages/iss/generator.py", line 240, in worker_iterator
    simulate_reads(
  File "/projectnb/talbot-lab-data/zrwerbin/.conda/envs/insilicoseq/lib/python3.10/site-packages/iss/generator.py", line 61, in simulate_reads
    for forward_record, reverse_record, mutations in reads_generator(
  File "/projectnb/talbot-lab-data/zrwerbin/.conda/envs/insilicoseq/lib/python3.10/site-packages/iss/generator.py", line 75, in reads_generator
    forward, reverse, mutations = simulate_read(record, error_model, i, cpu_number, sequence_type)
  File "/projectnb/talbot-lab-data/zrwerbin/.conda/envs/insilicoseq/lib/python3.10/site-packages/iss/generator.py", line 180, in simulate_read
    Seq(rev_comp(str(sequence[reverse_start:reverse_end]))),
  File "/projectnb/talbot-lab-data/zrwerbin/.conda/envs/insilicoseq/lib/python3.10/site-packages/iss/util.py", line 90, in rev_comp
    complement = "".join([bases[b] for b in sequence])
  File "/projectnb/talbot-lab-data/zrwerbin/.conda/envs/insilicoseq/lib/python3.10/site-packages/iss/util.py", line 90, in <listcomp>
    complement = "".join([bases[b] for b in sequence])
KeyError: 'x'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/projectnb/talbot-lab-data/zrwerbin/.conda/envs/insilicoseq/bin/iss", line 8, in <module>
    sys.exit(main())
  File "/projectnb/talbot-lab-data/zrwerbin/.conda/envs/insilicoseq/lib/python3.10/site-packages/iss/app.py", line 454, in main
    args.func(args)
  File "/projectnb/talbot-lab-data/zrwerbin/.conda/envs/insilicoseq/lib/python3.10/site-packages/iss/app.py", line 100, in generate_reads
    pool.starmap(
  File "/projectnb/talbot-lab-data/zrwerbin/.conda/envs/insilicoseq/lib/python3.10/multiprocessing/pool.py", line 375, in starmap
    return self._map_async(func, iterable, starmapstar, chunksize).get()
  File "/projectnb/talbot-lab-data/zrwerbin/.conda/envs/insilicoseq/lib/python3.10/multiprocessing/pool.py", line 774, in get
    raise self._value
KeyError: 'x'
(insilicoseq)[zrwerbin@scc-up2 01_mock_community_input]$ 

(insilicoseq)[zrwerbin@scc-up2 01_mock_community_input]$ conda list
# packages in environment at /projectnb/talbot-lab-data/zrwerbin/.conda/envs/insilicoseq:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
biopython                 1.83            py310h2372a71_0    conda-forge
brotli-python             1.1.0           py310hc6cd4ac_1    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.26.0               hd590300_0    conda-forge
ca-certificates           2024.2.2             hbcca054_0    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
future                    1.0.0              pyhd8ed1ab_0    conda-forge
idna                      3.6                pyhd8ed1ab_0    conda-forge
insilicoseq               2.0.1                    pypi_0    pypi
joblib                    1.3.2              pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libblas                   3.9.0           21_linux64_openblas    conda-forge
libcblas                  3.9.0           21_linux64_openblas    conda-forge
libcurl                   8.5.0                hca28451_0    conda-forge
libdeflate                1.18                 h0b41bf4_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_5    conda-forge
libgfortran-ng            13.2.0               h69a702a_5    conda-forge
libgfortran5              13.2.0               ha4646dd_5    conda-forge
libgomp                   13.2.0               h807b86a_5    conda-forge
liblapack                 3.9.0           21_linux64_openblas    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge

openssl                   3.2.1                hd590300_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.26          pthreads_h413a1c8_0    conda-forge
libsqlite                 3.45.1               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_5    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
ncurses                   6.4                  h59595ed_2    conda-forge
numpy                     1.26.4          py310hb13e2d6_0    conda-forge
openssl                   3.2.1                hd590300_0    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pysam                     0.22.0          py310h41dec4a_0    bioconda
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.13         hd12c33a_1_cpython    conda-forge
python_abi                3.10                    4_cp310    conda-forge
readline                  8.2                  h8228510_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
scipy                     1.12.0          py310hb13e2d6_2    conda-forge
setuptools                69.1.0             pyhd8ed1ab_1    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
urllib3                   2.2.1              pyhd8ed1ab_0    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge