hifiasm module broke

[mbeavitt]

Description of bug

The hifiasm stderr log did not work with multiqc v1.19

File that triggers the error

Methanocorpusculum_labreanum_test.stderr.log

MultiQC Error log

/// MultiQC 🔍 | v1.19
  
  |           multiqc | Search path : /home/tubergene/nf-core-bhasm/work/d9/a7e07c700f58c4fa5b2fbfe078b54a
  |         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 15/15  
  |    custom_content | software_versions: Found 1 sample (html)
  |    custom_content | nf-core-bhasm-methods-description: Found 1 sample (html)
  |    custom_content | nf-core-bhasm-summary: Found 1 sample (html)
  ╭──────────────── Oops! The 'hifiasm' MultiQC module broke... ─────────────────╮
  │ Please copy this log and report it at                                        │
  │ https://github.com/ewels/MultiQC/issues                                      │
  │ Please attach a file that triggers the error. The last file found was:       │
  │ ./5/Methanocorpusculum_labreanum_test.stderr.log                             │
  │                                                                              │
  │ Traceback (most recent call last):                                           │
  │   File "/usr/local/lib/python3.11/site-packages/multiqc/multiqc.py", line 72 │
  │     output = mod()                                                           │
  │              ^^^^^                                                           │
  │   File "/usr/local/lib/python3.11/site-packages/multiqc/modules/hifiasm/hifi │
  │     self.parse_hifiasm_log_files()                                           │
  │   File "/usr/local/lib/python3.11/site-packages/multiqc/modules/hifiasm/hifi │
  │     data = self.extract_kmer_graph(f["f"])                                   │
  │            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^                                   │
  │   File "/usr/local/lib/python3.11/site-packages/multiqc/modules/hifiasm/hifi │
  │     count = int(spline[3])                                                   │
  │                 ~~~~~~^^^                                                    │
  │ IndexError: list index out of range                                          │
  │                                                                              │
  ╰──────────────────────────────────────────────────────────────────────────────╯
  |          nanostat | Found 1 reports
  |           multiqc | Report      : multiqc_report.html
  |           multiqc | Data        : multiqc_data
  |           multiqc | Plots       : multiqc_plots
  |           multiqc | MultiQC complete

Before submitting

• I have read the troubleshooting documentation.
• I am using the latest release of MultiQC.
• I have included a full MultiQC log, not truncated.
• I have attached an input file (.zip if necessary) that triggers the error.

[mbeavitt]

please ignore the fact that I have some weird flags in the initial command - I know bacteria are not tetraploid but this is test data for a larger pipeline :)

[mbeavitt]

Aha, found the issue. I think it's perhaps because I'm using a small pacbio input file, and so sometimes there are no asterisks in the log file line. The code in the hifiasm module's extract_kmer_graph function can be updated to:

def extract_kmer_graph(fin):
    """Extract the kmer graph from file in"""
    data = dict()

    found_histogram = False

    for line in fin:
        if line.startswith("[M::ha_hist_line]"):
            found_histogram = True
            spline = line.strip().split()
            # Occurrence of kmer
            occurrence = spline[1][:-1]
            # Special case
            if occurrence == "rest":
                continue
            # Count of the occurrence
            print(spline)
            if "*" in spline[2]:
                count = int(spline[3])
            else:
                count = int(spline[2])
            data[int(occurrence)] = count
            print(data)
        # If we are no longer in the histogram
        elif found_histogram:
            return data

Before:

                count = int(spline[3])

After:

            if "*" in spline[2]:
                count = int(spline[3])
            else:
                count = int(spline[2])

[mbeavitt]

I made a PR:

#2268

[vladsavelyev]

Thanks a lot @mbeavitt for a detailed bug report, and even for contributing a fix 🙏