🧬 fixed downloading and cleanup

example/README.md

@@ -2,72 +2,74 @@
 
 GMWI2 (Gut Microbiome Wellness Index 2) is a robust and biologically interpretable predictor of health status based on gut microbiome taxonomic profiles.
 
-Below is a mini-tutorial on how to download a metagenome sample (run accession SRR1761666, a healthy sample belonging to the pooled dataset of 8,069 stool metagenomes used to trained GMWI2) from the Sequence Read Archive (SRA) and use this command-line tool on the downloaded .fastq files to compute the GMWI2 score.
+Below is a mini-tutorial on how to download a metagenome sample (run accession SRR1761667, a healthy sample belonging to the pooled dataset of 8,069 stool metagenomes used to trained GMWI2) from the Sequence Read Archive (SRA) and use this command-line tool on the downloaded .fastq files to compute the GMWI2 score.
 
 ## Download and uncompress fastq files using [sra-tools](https://github.com/ncbi/sra-tools/wiki/)
 
 ```bash
-prefetch SRR1761666
-cd SRR1761666
-fasterq-dump SRR1761666.sra --skip-technical --split-files
+prefetch SRR1761667
+cd SRR1761667
+fasterq-dump SRR1761667.sra --skip-technical --split-files
 ```
 
 Output:
 ```bash
 .
-├── SRR1761666.sra
-├── SRR1761666_1.fastq
-└── SRR1761666_2.fastq
+├── SRR1761667.sra
+├── SRR1761667_1.fastq
+└── SRR1761667_2.fastq
 ```
 
 ## Run GMWI2 on the extracted paired-end metagenome reads using 16 threads
 ```bash
-gmwi2 -i SRR1761666_1.fastq,SRR1761666_2.fastq -n 16 -o SRR1761666
+gmwi2 -f SRR1761667_1.fastq -r SRR1761667_2.fastq -n 16 -o SRR1761667
 ```
 
 Output:
 ```bash
 .
-├── SRR1761666.sra
-├── SRR1761666_1.fastq
-├── SRR1761666_2.fastq
-├── SRR1761666_GMWI2.txt
-├── SRR1761666_GMWI2_taxa.txt
-└── SRR1761666_metaphlan.txt
+├── SRR1761667.sra
+├── SRR1761667_1.fastq
+├── SRR1761667_2.fastq
+├── SRR1761667_GMWI2.txt
+├── SRR1761667_GMWI2_taxa.txt
+└── SRR1761667_metaphlan.txt
 ```
 
 ## Verify that your output files are identical to those in this directory and shown below
 
+Note: Slight differences in the output may occur due to updates to the marker databases or differences in versions of dependencies.
+
 ```bash
 head *.txt
 ```
 
 Output:
 ```bash
-==> SRR1761666_GMWI2.txt <==
-1.8352371587787006
+==> SRR1761667_GMWI2.txt <==
+1.4017773651306447
 
-==> SRR1761666_GMWI2_taxa.txt <==
-taxa_name	coefficient
-k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces	-0.002971706718511846
-k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales	0.10985985383440176
-k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae	0.058580915614315394
-k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri	0.019327473574940728
-k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_sp_AM42_24	0.20713868303104763
-k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae	-0.016769603426408927
-k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium_eligens	0.15173013105151076
-k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium_hallii	0.05692133949999932
-k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Blautia|s__Ruminococcus_torques	0.14658685040674785
+==> SRR1761667_GMWI2_taxa.txt <==
+taxa_name       coefficient
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_adolescentis       0.184438966271142
+k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales       0.10985985383440176
+k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Eggerthellales|f__Eggerthellaceae    0.058580915614315394
+k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_vulgatus   -0.07104784193156662
+k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri        0.019327473574940728
+k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_sp_AM42_24   0.20713868303104763
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae      -0.016769603426408927
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium_hallii 0.05692133949999932
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium_sp_CAG_180     -0.284991033861398
 
-==> SRR1761666_metaphlan.txt <==
+==> SRR1761667_metaphlan.txt <==
 #mpa_v30_CHOCOPhlAn_201901
-#/Users/daniel/opt/anaconda3/envs/gmwi2_env/bin/metaphlan SRR1761666_1.fastq,SRR1761666_2.fastq --index mpa_v30_CHOCOPhlAn_201901 --bowtie2out bowtie2out.bowtie2.bz2 --nproc 16 --input_type fastq -o SRR1761666_metaphlan.txt --add_viruses --unknown_estimation
-#SampleID	Metaphlan_Analysis
-#clade_name	NCBI_tax_id	relative_abundance	additional_species
-UNKNOWN	-1	61.19317	
-k__Bacteria	2	38.73979484943826	
-k__Viruses	10239	0.0670310303421447	
-k__Bacteria|p__Bacteroidetes	2|976	20.26310443428757	
-k__Bacteria|p__Firmicutes	2|1239	15.384543125636853	
-k__Bacteria|p__Actinobacteria	2|201174	3.067314801633372	
+#/Users/daniel/opt/anaconda3/envs/gmwi2_env/bin/metaphlan SRR1761667_QC_1P.fastq.gz,SRR1761667_QC_2P.fastq.gz --index mpa_v30_CHOCOPhlAn_201901 --force --no_map --nproc 16 --input_type fastq -o SRR1761667_metaphlan.txt --add_viruses --unknown_estimation
+#SampleID       Metaphlan_Analysis
+#clade_name     NCBI_tax_id     relative_abundance      additional_species
+UNKNOWN -1      70.84224
+k__Bacteria     2       29.031894900524044
+k__Archaea      2157    0.1258623750557678
+k__Bacteria|p__Firmicutes       2|1239  11.989174109844733
+k__Bacteria|p__Proteobacteria   2|1224  11.783008355476293
+k__Bacteria|p__Bacteroidetes    2|976   4.101251412438412
 ```