[2024-01-24 12:15:03,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:03,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:03,965] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ccd3eb0-9531-4ad1-8125-0498780a9dbd/dqc_reference
[2024-01-24 12:15:05,226] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,227] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,228] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c4f1fc2-2629-4f6c-a17a-77c0bf2ae84f/GCF_018854495.1_ASM1885449v1_genomic.fna.gz | prodigal -d GCF_018854495.1_ASM1885449v1_genomic.fna/cds.fna -a GCF_018854495.1_ASM1885449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:13,506] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:13,506] [INFO] Task started: HMMsearch
[2024-01-24 12:15:13,507] [INFO] Running command: hmmsearch --tblout GCF_018854495.1_ASM1885449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ccd3eb0-9531-4ad1-8125-0498780a9dbd/dqc_reference/reference_markers.hmm GCF_018854495.1_ASM1885449v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:13,734] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:13,735] [INFO] Found 6/6 markers.
[2024-01-24 12:15:13,764] [INFO] Query marker FASTA was written to GCF_018854495.1_ASM1885449v1_genomic.fna/markers.fasta
[2024-01-24 12:15:13,765] [INFO] Task started: Blastn
[2024-01-24 12:15:13,765] [INFO] Running command: blastn -query GCF_018854495.1_ASM1885449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ccd3eb0-9531-4ad1-8125-0498780a9dbd/dqc_reference/reference_markers.fasta -out GCF_018854495.1_ASM1885449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:14,449] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:14,453] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:14,453] [INFO] Target genome list was writen to GCF_018854495.1_ASM1885449v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:14,457] [INFO] Task started: fastANI
[2024-01-24 12:15:14,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c4f1fc2-2629-4f6c-a17a-77c0bf2ae84f/GCF_018854495.1_ASM1885449v1_genomic.fna.gz --refList GCF_018854495.1_ASM1885449v1_genomic.fna/target_genomes.txt --output GCF_018854495.1_ASM1885449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:22,650] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:22,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ccd3eb0-9531-4ad1-8125-0498780a9dbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:22,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ccd3eb0-9531-4ad1-8125-0498780a9dbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:22,657] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:22,657] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:22,657] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Acidithiobacillus ferrooxidans	strain=ATCC 23270	GCA_000021485.1	920	920	type	True	94.4402	656	877	95	below_threshold
Acidithiobacillus ferridurans	strain=JCM 18981	GCA_003966655.1	1232575	1232575	type	True	94.2234	644	877	95	below_threshold
Acidithiobacillus ferridurans	strain=ATCC 33020	GCA_018854555.1	1232575	1232575	type	True	93.9336	596	877	95	below_threshold
Acidithiobacillus ferriphilus	strain=DSM 100412	GCA_018854775.1	1689834	1689834	type	True	85.0902	437	877	95	below_threshold
Acidithiobacillus ferrianus	strain=MG	GCA_010378095.1	2678518	2678518	type	True	82.1124	455	877	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:22,659] [INFO] DFAST Taxonomy check result was written to GCF_018854495.1_ASM1885449v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:22,660] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:22,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:22,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ccd3eb0-9531-4ad1-8125-0498780a9dbd/dqc_reference/checkm_data
[2024-01-24 12:15:22,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:22,694] [INFO] Task started: CheckM
[2024-01-24 12:15:22,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018854495.1_ASM1885449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018854495.1_ASM1885449v1_genomic.fna/checkm_input GCF_018854495.1_ASM1885449v1_genomic.fna/checkm_result
[2024-01-24 12:15:51,676] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:51,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:51,699] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:51,700] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:51,700] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018854495.1_ASM1885449v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:51,700] [INFO] Task started: Blastn
[2024-01-24 12:15:51,700] [INFO] Running command: blastn -query GCF_018854495.1_ASM1885449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ccd3eb0-9531-4ad1-8125-0498780a9dbd/dqc_reference/reference_markers_gtdb.fasta -out GCF_018854495.1_ASM1885449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:52,865] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:52,868] [INFO] Selected 6 target genomes.
[2024-01-24 12:15:52,868] [INFO] Target genome list was writen to GCF_018854495.1_ASM1885449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:52,873] [INFO] Task started: fastANI
[2024-01-24 12:15:52,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c4f1fc2-2629-4f6c-a17a-77c0bf2ae84f/GCF_018854495.1_ASM1885449v1_genomic.fna.gz --refList GCF_018854495.1_ASM1885449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018854495.1_ASM1885449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:57,218] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:57,224] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:57,224] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_018854495.1	s__Acidithiobacillus ferrooxidans_C	100.0	871	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000021485.1	s__Acidithiobacillus ferrooxidans	94.5011	654	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	98.94	96.59	0.87	0.73	15	-
GCF_003966655.1	s__Acidithiobacillus ferridurans	94.1931	645	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.15	97.49	0.87	0.83	8	-
GCF_018853935.1	s__Acidithiobacillus ferrivorans	85.6429	564	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	96.97	95.59	0.71	0.67	8	-
GCF_018854775.1	s__Acidithiobacillus ferriphilus	85.0722	438	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	98.36	97.93	0.81	0.77	8	-
GCF_010378095.1	s__Acidithiobacillus ferrianus	82.1241	454	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:57,226] [INFO] GTDB search result was written to GCF_018854495.1_ASM1885449v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:57,226] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:57,229] [INFO] DFAST_QC result json was written to GCF_018854495.1_ASM1885449v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:57,229] [INFO] DFAST_QC completed!
[2024-01-24 12:15:57,229] [INFO] Total running time: 0h0m53s