plassembler: insufficient read depth

[fredjaya]

Describe the bug
plassembler fails when running barcode24 from the companion animal data. Error thrown is due to insufficient coverage but unclear due to i.e. prophages.

To Reproduce
Run barcode24 using the issue-54 branch pipeline 2e9e869 on Gadi

Output

  2024-11-06 00:36:34.565 | ERROR    | plassembler:long:1446 - No chromosome was identified. Likely, there was insufficient long read depth to assemble a chromosome.
  Increasing sequencing depth is recommended.
  Also please check your -c or --chromosome parameter, it may be too high

Show full output:

Caused by:
  Process `plassembler (DETECTING PLASMIDS AND OTHER MOBILE ELEMENTS: barcode24)` terminated with an error exit status (1)


Command executed:

  plassembler long \
    -d plasmid_db_plassembler \
   -l barcode24_trimmed.fastq.gz \
    --flye_assembly barcode24_flye_assembly/assembly.fasta \
    --flye_info barcode24_flye_assembly/assembly_info.txt \
    -o barcode24_plassembler \
    -t 16 -f

  # Check if the resulting .fasta file is empty
  if [ -s barcode24_plassembler/plassembler_plasmids.fasta ]; then
    echo "The .fasta file contains plasmid sequence. Proceeding with output."
  else
    echo "The .fasta file is empty, no plasmids detected. Removing from output."
    rm -f barcode24_plassembler/plassembler_plasmids.fasta
  fi

Command exit status:
  1

Command output:
  (empty)

Command exit status:
  1

Command output:
  (empty)

Command error:
  2024-11-06 00:36:18.608 | INFO     | plassembler.utils.db:check_db_installation:54 - PLSDB Database at plasmid_db_plassembler has already been downloaded
  2024-11-06 00:36:18.608 | INFO     | plassembler:long:1324 - Database successfully checked.
  2024-11-06 00:36:18.609 | INFO     | plass read quality is 9
  2024-11-06 00:36:16.689 | INFO     | plassembler:long:1300 - Thread count is 16
  2024-11-06 00:36:16.689 | INFO     | plassembler:long:1301 - --force is True
  2024-11-06 00:36:16.689 | INFO     | plassembler:long:1302 - --skip_qc is False
  2024-11-06 00:36:16.689 | INFO     | plassembler:long:1303 - --raw_flag is False
  2024-11-06 00:36:16.689 | INFO     | plassembler:long:1304 - --pacbio_model is nothing
  2024-11-06 00:36:16.689 | INFO     | plassembler:long:1305 - --keep_chromosome is False
  2024-11-06 00:36:16.690 | INFO     | plassembler:long:1306 - --flye_directory is nothing
  2024-11-06 00:36:16.690 | INFO     | plassembler:long:1307 - --flye_assembly is barcode24_flye_assembly/assembly.fasta
  2024-11-06 00:36:16.690 | INFO     | plassembler:long:1308 - --flye_info is barcode24_flye_assembly/assembly_info.txt
  2024-11-06 00:36:16.690 | INFO     | plassembler:long:1309 - --corrected_error_rate is 0.12
  2024-11-06 00:36:16.690 | INFO     | plassembler:long:1310 - --no_chromosome is False
  2024-11-06 00:36:16.690 | INFO     | plassembler:long:1311 - --depth_filter is 0.25
  2024-11-06 00:36:16.690 | INFO     | plassembler:long:1312 - --unicycler_options is None
  2024-11-06 00:36:16.690 | INFO     | plassembler:long:1313 - --spades_options is None
  2024-11-06 00:36:16.690 | INFO     | plassembler:long:1317 - Checking dependencies
  2024-11-06 00:36:16.764 | INFO     | plassembler.utils.input_commands:check_dependencies:199 - Flye version found is v2.9.3-b1797.
  2024-11-06 00:36:16.765 | INFO     | plassembler.utils.input_commands:check_dependencies:209 - Flye version is ok.
  2024-11-06 00:36:16.781 | INFO     | plassembler.utils.input_commands:check_dependencies:218 - Raven v1.8.3 found.
  2024-11-06 00:36:16.781 | INFO     | plassembler.utils.input_commands:check_dependencies:220 - Raven version is ok.
  2024-11-06 00:36:17.080 | INFO     | plassembler.utils.input_commands:check_dependencies:242 - Unicycler version found is v0.5.0.
  2024-11-06 00:36:17.081 | INFO     | plassembler.utils.input_commands:check_dependencies:255 - Unicycler version is ok.
  2024-11-06 00:36:17.315 | INFO     | plassembler.utils.input_commands:check_dependencies:265 - SPAdes v3.15.4 found.
  2024-11-06 00:36:17.362 | INFO     | plassembler.utils.input_commands:check_dependencies:278 - Samtools v1.18 found.
  2024-11-06 00:36:17.372 | INFO     | plassembler.utils.input_commands:check_dependencies:289 - minimap2 v2.27-r1193 found.
  2024-11-06 00:36:17.384 | INFO     | plassembler.utils.input_commands:check_dependencies:300 - fastp v0.23.4 found.
  2024-11-06 00:36:17.400 | INFO     | plassembler.utils.input_commands:check_dependencies:311 - chopper v0.7.0 found.
  2024-11-06 00:36:17.420 | INFO     | plassembler.utils.input_commands:check_dependencies:326 - mash v2.3 found.
  2024-11-06 00:36:17.551 | INFO     | plassembler.utils.input_commands:check_dependencies:337 - canu v2.2 found.
  2024-11-06 00:36:18.114 | INFO     | plassembler.utils.input_commands:check_dependencies:348 - dnaapler v0.7.0 found.
  2024-11-06 00:36:18.605 | INFO     | plassembler.utils.input_commands:check_dependencies:365 - BLAST version found is v2.15.0.
  2024-11-06 00:36:18.606 | INFO     | plassembler.utils.input_commands:check_dependencies:371 - All dependencies found.
  2024-11-06 00:36:18.607 | INFO     | plassembler:long:1321 - Checking database installation.
  2024-11-06 00:36:18.607 | INFO     | plassembler.utils.db:check_db_installation:52 - PLSDB Database mash sketch at plasmid_db_plassembler/plsdb_2023_11_03_v2.msh exists.
  2024-11-06 00:36:18.608 | INFO     | plassembler.utils.db:check_db_installation:53 - PLSDB Database tsv metadata file at plasmid_db_plassembler/plsdb_2023_11_03_v2.tsv exists.
  2024-11-06 00:36:18.608 | INFO     | plassembler.utils.db:check_db_installation:54 - PLSDB Database at plasmid_db_plassembler has already been downloaded
  2024-11-06 00:36:18.608 | INFO     | plassembler:long:1324 - Database successfully checked.
  2024-11-06 00:36:18.609 | INFO     | plassembler:long:1327 - Checking input fastqs.
  2024-11-06 00:36:18.624 | INFO     | plassembler.utils.input_commands:validate_fastq:24 - FASTQ barcode24_trimmed.fastq.gz checked
  2024-11-06 00:36:18.625 | INFO     | plassembler:long:1350 - Filtering long reads with chopper
  2024-11-06 00:36:18.625 | INFO     | plassembler.utils.qc:chopper:25 - Started running chopper
  2024-11-06 00:36:34.480 | INFO     | plassembler.utils.qc:chopper:82 - Finished running chopper
  2024-11-06 00:36:34.482 | INFO     | plassembler:long:1391 - You have specified a barcode24_flye_assembly/assembly.fasta and barcode24_flye_assembly/assembly_info.txt from an existing flye assembly.
  2024-11-06 00:36:34.512 | INFO     | plassembler:long:1421 - Counting Contigs.
  2024-11-06 00:36:34.532 | INFO     | plassembler.utils.plass_class:get_contig_count:87 - Assembled 9 contigs.
  2024-11-06 00:36:34.565 | ERROR    | plassembler:long:1446 - No chromosome was identified. Likely, there was insufficient long read depth to assemble a chromosome.
  Increasing sequencing depth is recommended.
  Also please check your -c or --chromosome parameter, it may be too high

Work dir:
  /scratch/tj48/fj9712/02_work/2411_catdogs/work/d7/860ffc9767e41c973476e81921c287

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

Additional context
Possibly related to #59