[2024-01-24 11:59:51,993] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:51,995] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:51,995] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb534a78-3124-4a84-b282-498988778dea/dqc_reference
[2024-01-24 11:59:55,380] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:55,381] [INFO] Task started: Prodigal
[2024-01-24 11:59:55,382] [INFO] Running command: gunzip -c /var/lib/cwl/stgf85388c5-869b-4f84-aa6f-6571b02ec756/GCF_016653615.1_ASM1665361v1_genomic.fna.gz | prodigal -d GCF_016653615.1_ASM1665361v1_genomic.fna/cds.fna -a GCF_016653615.1_ASM1665361v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:01,132] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:01,133] [INFO] Task started: HMMsearch
[2024-01-24 12:00:01,133] [INFO] Running command: hmmsearch --tblout GCF_016653615.1_ASM1665361v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb534a78-3124-4a84-b282-498988778dea/dqc_reference/reference_markers.hmm GCF_016653615.1_ASM1665361v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:01,396] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:01,397] [INFO] Found 6/6 markers.
[2024-01-24 12:00:01,425] [INFO] Query marker FASTA was written to GCF_016653615.1_ASM1665361v1_genomic.fna/markers.fasta
[2024-01-24 12:00:01,426] [INFO] Task started: Blastn
[2024-01-24 12:00:01,426] [INFO] Running command: blastn -query GCF_016653615.1_ASM1665361v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb534a78-3124-4a84-b282-498988778dea/dqc_reference/reference_markers.fasta -out GCF_016653615.1_ASM1665361v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:02,040] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:02,044] [INFO] Selected 38 target genomes.
[2024-01-24 12:00:02,045] [INFO] Target genome list was writen to GCF_016653615.1_ASM1665361v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:02,097] [INFO] Task started: fastANI
[2024-01-24 12:00:02,097] [INFO] Running command: fastANI --query /var/lib/cwl/stgf85388c5-869b-4f84-aa6f-6571b02ec756/GCF_016653615.1_ASM1665361v1_genomic.fna.gz --refList GCF_016653615.1_ASM1665361v1_genomic.fna/target_genomes.txt --output GCF_016653615.1_ASM1665361v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:21,895] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:21,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb534a78-3124-4a84-b282-498988778dea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:21,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb534a78-3124-4a84-b282-498988778dea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:21,901] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:00:21,901] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:00:21,901] [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
Entomomonas moraniae	strain=QZS01	GCA_003991975.1	2213226	2213226	type	True	78.6523	312	1078	95	below_threshold
Thiopseudomonas alkaliphila	strain=B4199	GCA_001267175.1	1697053	1697053	type	True	78.3717	50	1078	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:21,903] [INFO] DFAST Taxonomy check result was written to GCF_016653615.1_ASM1665361v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:21,904] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:21,904] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:21,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb534a78-3124-4a84-b282-498988778dea/dqc_reference/checkm_data
[2024-01-24 12:00:21,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:21,937] [INFO] Task started: CheckM
[2024-01-24 12:00:21,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016653615.1_ASM1665361v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016653615.1_ASM1665361v1_genomic.fna/checkm_input GCF_016653615.1_ASM1665361v1_genomic.fna/checkm_result
[2024-01-24 12:00:45,383] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:45,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:45,407] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:45,408] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:45,408] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016653615.1_ASM1665361v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:45,409] [INFO] Task started: Blastn
[2024-01-24 12:00:45,409] [INFO] Running command: blastn -query GCF_016653615.1_ASM1665361v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb534a78-3124-4a84-b282-498988778dea/dqc_reference/reference_markers_gtdb.fasta -out GCF_016653615.1_ASM1665361v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:46,240] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:46,245] [INFO] Selected 36 target genomes.
[2024-01-24 12:00:46,245] [INFO] Target genome list was writen to GCF_016653615.1_ASM1665361v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:46,296] [INFO] Task started: fastANI
[2024-01-24 12:00:46,297] [INFO] Running command: fastANI --query /var/lib/cwl/stgf85388c5-869b-4f84-aa6f-6571b02ec756/GCF_016653615.1_ASM1665361v1_genomic.fna.gz --refList GCF_016653615.1_ASM1665361v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016653615.1_ASM1665361v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:10,707] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:10,711] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:10,712] [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_016653615.1	s__Entomomonas sp016653615	100.0	1077	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Entomomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003991975.1	s__Entomomonas moraniae	78.6476	313	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Entomomonas	95.0	96.47	96.47	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:10,713] [INFO] GTDB search result was written to GCF_016653615.1_ASM1665361v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:10,714] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:10,716] [INFO] DFAST_QC result json was written to GCF_016653615.1_ASM1665361v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:10,717] [INFO] DFAST_QC completed!
[2024-01-24 12:01:10,717] [INFO] Total running time: 0h1m19s