combining krakenuniq reports
Sabrin2020 opened this issue · 2 comments
Is this scripts could be working with krakenuniq reports? If yes how to fix it please
combine_kreports.py -r *-krakenuniq-report.tsv -o COMBINED.KREPORT --display-headers
STEP 1: READING REPORTS
1/301 samples processedTraceback (most recent call last):
File "/user/asga9989/.conda/envs/krakentools/bin/combine_kreports.py", line 311, in
main()
File "/user/asga9989/.conda/envs/krakentools/bin/combine_kreports.py", line 226, in main
while level_num != (prev_node.level_num + 1):
^^^^^^^^^^^^^^^^^^^
AttributeError: 'int' object has no attribute 'level_num'
head _PL17_99indbel-krakenuniq-report.tsv
# KrakenUniq v1.0.3 DATE:2023-08-06T00:57:24Z DB:/gss/work/asga9989/krakenuniq/microbial-nt DB_SIZE:706079654188 WD:/gss/work/asga9989/all_samples_run
# CL:/cm/shared/uniol/software/8.3/KrakenUniq/1.0.3-intel-2019b/bin/krakenuniq --db /gss/work/asga9989/krakenuniq/microbial-nt --threads 20 --fastq-input --gzip-compressed --paired --output 07_TAXONOMY_references_removed/_PL17_99indbel.krakenuniq --report-file 07_TAXONOMY_references_removed/_PL17_99indbel-krakenuniq-report.tsv 01_QC/_PL17_99indbel-FILTERED_R1.fastq.gz 01_QC/_PL17_99indbel-FILTERED_R2.fastq.gz
% reads taxReads kmers dup cov taxID rank taxName
43.16 783047 783047 132171775 3.13 NA 0 no rank unclassified
56.84 1031262 3084 504258 49.4 8.57e-06 1 no rank root
56.47 1024531 4231 491054 20.4 8.674e-06 131567 no rank cellular organisms
54.03 980284 199152 475276 13.8 1.16e-05 2 superkingdom Bacteria
31.88 578351 139858 424790 6.27 2.301e-05 1224 phylum Pseudomonadota
12.22 221695 129781 337596 4.34 3.528e-05 1236 class Gammaproteobacteria
3.011 54630 7 1869 62.1 7.733e-07 91347 order Enterobacterales
The script should work for kuniq reports but I'll check.
Hi there, I am also having the same error code when trying to combine my krakenuniq reportfiles. Is there a resolution for this?
Thank you for your help!