Hi, I am getting no errors so far. But when I add a kraken report file, I get the following error.
(sneakernet) [gzu2@monolith3 MultiQC-build]$ multiqc . --force
/// MultiQC � | v1.17
| multiqc | Search path : /scicomp/groups-pure/OID/NCEZID/DFWED/EDLB/projects/ont-pn-validation/AR_Bank-Illumina/shortreads/Campy/SneakerNet/MultiQC-build
| searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 10/10
| custom_content | addReadMetrics': Found 10 samples (bargraph)
| custom_content | sn_mlst': Found 5 samples (table)
| custom_content | sn_detectContamination-kraken': Found 5 samples (table)
| custom_content | baseBalance': Found 20 samples (bargraph)
| custom_content | sn_staramr': Found 5 samples (table)
| custom_content | sn_passfail': Found 5 samples (table)
| custom_content | sn_detectContamination-mlst': Found 5 samples (table)
╭──────────────────────────────────────────────── Oops! The 'kraken' 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: ./foobar.report │
│ │
│ Traceback (most recent call last): │
│ File "/scicomp/home-pure/gzu2/bin/miniconda3/envs/sneakernet/lib/python3.9/site-packages/multiqc/multiqc.py", line 689, in run │
│ output = mod() │
│ File "/scicomp/home-pure/gzu2/bin/miniconda3/envs/sneakernet/lib/python3.9/site-packages/multiqc/modules/kraken/kraken.py", line 51, in │
│ for f in self.find_log_files(self.anchor, filehandles=True): │
│ File "/scicomp/home-pure/gzu2/bin/miniconda3/envs/sneakernet/lib/python3.9/site-packages/multiqc/modules/base_module.py", line 139, in f │
│ for f in report.files[sp_key]: │
│ KeyError: 'kraken-1' │
│ │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
| multiqc | Report : multiqc_report.html (overwritten)
| multiqc | Data : multiqc_data (overwritten)
| multiqc | MultiQC complete
This is the content of foobar.report
5.00 21431 21431 U 0 unclassified
95.00 407300 623 - 1 root
94.86 406677 0 - 131567 cellular organisms
94.85 406662 5806 D 2 Bacteria
93.30 399988 249 P 1224 Proteobacteria
93.17 399430 5 - 68525 delta/epsilon subdivisions
93.16 399425 0 C 29547 Epsilonproteobacteria
93.16 399425 696 O 213849 Campylobacterales
93.00 398712 1045 F 72294 Campylobacteraceae
92.72 397503 62770 G 194 Campylobacter
71.77 307703 26611 S 197 Campylobacter jejuni
65.56 281092 281092 - 32022 Campylobacter jejuni subsp. jejuni
4.14 17743 17743 S 195 Campylobacter coli