Error while running confinder

[ryobon-dev]

When I run confindr for the example-data, which you provided, I got the error in below.

Could you please help me to resolve this issue ?

(confindr) kansensho@DESKTOP-QBEDU0F:/mnt/e/Desktop/genome_analysis/T3OSK$ confindr.py -i example-data -o output -d DATABASES 2023-02-07 15:42:27 Welcome to ConFindr 0.3.2! Beginning analysis of your samples... 2023-02-07 15:42:27 Beginning analysis of sample example... 2023-02-07 15:42:27 Checking for cross-species contamination... 2023-02-07 15:42:27 Extracting rMLST genes... 2023-02-07 15:42:27 Quality trimming... 2023-02-07 15:42:27 Beginning 3 cycles of contamination detection... 2023-02-07 15:42:27 Working on cycle 1 of 3... Traceback (most recent call last): File "/home/kansensho/miniconda3/envs/confindr/bin/confindr.py", line 726, in find_contamination(pair, args) File "/home/kansensho/miniconda3/envs/confindr/bin/confindr.py", line 433, in find_contamination tmpdir=os.path.join(sample_tmp_dir, 'tmp'), logfile=log) File "/home/kansensho/miniconda3/envs/confindr/bin/confindr.py", line 194, in generate_kmers kmer_size=kmer_size, options='--bf-size 100M', returncmd=True) File "/home/kansensho/miniconda3/envs/confindr/lib/python3.6/site-packages/confindr_wrappers/jellyfish.py", line 65, in count forward_in = uncompress_gzip(forward_in) File "/home/kansensho/miniconda3/envs/confindr/lib/python3.6/site-packages/confindr_wrappers/jellyfish.py", line 11, in uncompress_gzip with gzip.open(infile, 'rb') as f: File "/home/kansensho/miniconda3/envs/confindr/lib/python3.6/gzip.py", line 53, in open binary_file = GzipFile(filename, gz_mode, compresslevel) File "/home/kansensho/miniconda3/envs/confindr/lib/python3.6/gzip.py", line 163, in init fileobj = self.myfileobj = builtins.open(filename, mode or 'rb') FileNotFoundError: [Errno 2] No such file or directory: 'output/example/subsample_0_R1.fastq.gz' (confindr) kansensho@DESKTOP-QBEDU0F:/mnt/e/Desktop/genome_analysis/T3OSK$

[ryobon-dev]

I am sending confindr_log.txt so that you can understand the situation.

confindr_log.txt

[pcrxn]

Hi @ryobon-dev, could you please update to the most recent release of ConFindr (v0.7.4) and then attempt the test again? Using Conda for installation: conda create -n confindr -c bioconda confindr=0.7.4 && conda activate confindr

[ryobon-dev]

It works ! Thank you very much for your rapid response.