Plassembler stops at Processing Sam/Bam Files and extracting Fastqs

Hi @gbouras13,

Many thanks for your excellent tool. I am trying to implement Plassembler (v1.6.2) within one of my in-house Nextflow pipelines on a Linux machine. Plassembler analysis ran successfully for one of two genomes of interest. For the second genome, Plassembler stopped at the processing Sam/Bam Files and extracting Fastqs step. Kindly find the error message below.

 2024-05-10 17:24:08.037 | INFO     | plassembler:run:793 - Mapping short reads.
  2024-05-10 17:24:08.037 | INFO     | plassembler.utils.external_tools:run_to_stdout:67 - Started running minimap2 -ax sr -t 1 15059/flye_renamed.fasta 15059/trimmed_R1.fastq 15059/trimmed_R2.fastq ...
  2024-05-10 17:25:00.741 | INFO     | plassembler.utils.external_tools:run_to_stdout:69 - Done running minimap2 -ax sr -t 1 15059/flye_renamed.fasta 15059/trimmed_R1.fastq 15059/trimmed_R2.fastq
2024-05-10 17:25:00.742 | INFO     | plassembler:run:800 - Processing Sam/Bam Files and extracting Fastqs. 
Traceback (most recent call last):
    File "/MIGE/04_PROJECTS/DAIKOS/longread_analysis/work/conda/plassembler-2a63b87dbbb2cd95edb41776d561fd4c/bin/plassembler", line 10, in <module>
      sys.exit(main())
    File "/MIGE/04_PROJECTS/DAIKOS/longread_analysis/work/conda/plassembler-2a63b87dbbb2cd95edb41776d561fd4c/lib/python3.9/site-packages/plassembler/__init__.py", line 1666, in main
      main_cli()
    File "/MIGE/04_PROJECTS/DAIKOS/longread_analysis/work/conda/plassembler-2a63b87dbbb2cd95edb41776d561fd4c/lib/python3.9/site-packages/click/core.py", line 1157, in __call__
      return self.main(*args, **kwargs)
    File "/MIGE/04_PROJECTS/DAIKOS/longread_analysis/work/conda/plassembler-2a63b87dbbb2cd95edb41776d561fd4c/lib/python3.9/site-packages/click/core.py", line 1078, in main
      rv = self.invoke(ctx)
    File "/MIGE/04_PROJECTS/DAIKOS/longread_analysis/work/conda/plassembler-2a63b87dbbb2cd95edb41776d561fd4c/lib/python3.9/site-packages/click/core.py", line 1688, in invoke
      return _process_result(sub_ctx.command.invoke(sub_ctx))
    File "/MIGE/04_PROJECTS/DAIKOS/longread_analysis/work/conda/plassembler-2a63b87dbbb2cd95edb41776d561fd4c/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
      return ctx.invoke(self.callback, **ctx.params)
    File "/MIGE/04_PROJECTS/DAIKOS/longread_analysis/work/conda/plassembler-2a63b87dbbb2cd95edb41776d561fd4c/lib/python3.9/site-packages/click/core.py", line 783, in invoke
      return __callback(*args, **kwargs)
    File "/MIGE/04_PROJECTS/DAIKOS/longread_analysis/work/conda/plassembler-2a63b87dbbb2cd95edb41776d561fd4c/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func
      return f(get_current_context(), *args, **kwargs)
    File "/MIGE/04_PROJECTS/DAIKOS/longread_analysis/work/conda/plassembler-2a63b87dbbb2cd95edb41776d561fd4c/lib/python3.9/site-packages/plassembler/__init__.py", line 804, in run
      extract_long_fastqs_slow_keep_fastqs(outdir, samfile, plasmidfastqs)
    File "/MIGE/04_PROJECTS/DAIKOS/longread_analysis/work/conda/plassembler-2a63b87dbbb2cd95edb41776d561fd4c/lib/python3.9/site-packages/plassembler/utils/sam_to_fastq.py", line 92, in extract_long_fastqs_slow_keep_fastqs
      "".join(chr(q + 33) for q in quality) + "\n"
  TypeError: 'NoneType' object is not iterable

The bash command;

#!/bin/bash -ue
plassembler run \
        \
-d plassembler_db \
-l 15059.fastq.gz \
-1 15059_1.fastq.gz \
-2 15059_2.fastq.gz \
-m 1  \
-p 15059  \
-o 15059 \
--keep_fastqs \
--keep_chromosome  \
       -r \

My guess is that there are no fastqs to be extracted by Plassembler (using the --keep_fastqs argument). Is this correct? If so, does this mean that no plasmids are present in this genome? If truly there are no plasmids, is it then possible that an empty fastq file (e.g., within the plasmid_fastqs directory) is produced and the run continues with a warning message in the logs rather than stopping altogether (thinking Nextflow/Snakemake application)?

Start with plassembler/utils/sam_to_fastq.py, especially extract_long_fastqs_slow_keep_fastqs, using the traceback and the --keep_fastqs invocation as the reproduction path. Check how records without iterable quality data are handled and verify the run no longer raises TypeError when no fastqs can be extracted, while producing the requested warning or empty output behavior.