[2024-01-24 13:28:00,793] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:00,794] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:00,795] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f872e2f-30d7-490e-8b13-5cfbe9e33440/dqc_reference
[2024-01-24 13:28:02,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:02,086] [INFO] Task started: Prodigal
[2024-01-24 13:28:02,086] [INFO] Running command: gunzip -c /var/lib/cwl/stg2793d6f0-e99e-4075-957b-88e822b9da4b/GCF_014042165.1_ASM1404216v1_genomic.fna.gz | prodigal -d GCF_014042165.1_ASM1404216v1_genomic.fna/cds.fna -a GCF_014042165.1_ASM1404216v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:16,200] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:16,200] [INFO] Task started: HMMsearch
[2024-01-24 13:28:16,200] [INFO] Running command: hmmsearch --tblout GCF_014042165.1_ASM1404216v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f872e2f-30d7-490e-8b13-5cfbe9e33440/dqc_reference/reference_markers.hmm GCF_014042165.1_ASM1404216v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:16,448] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:16,449] [INFO] Found 6/6 markers.
[2024-01-24 13:28:16,474] [INFO] Query marker FASTA was written to GCF_014042165.1_ASM1404216v1_genomic.fna/markers.fasta
[2024-01-24 13:28:16,474] [INFO] Task started: Blastn
[2024-01-24 13:28:16,474] [INFO] Running command: blastn -query GCF_014042165.1_ASM1404216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f872e2f-30d7-490e-8b13-5cfbe9e33440/dqc_reference/reference_markers.fasta -out GCF_014042165.1_ASM1404216v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:17,109] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:17,114] [INFO] Selected 22 target genomes.
[2024-01-24 13:28:17,115] [INFO] Target genome list was writen to GCF_014042165.1_ASM1404216v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:17,130] [INFO] Task started: fastANI
[2024-01-24 13:28:17,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg2793d6f0-e99e-4075-957b-88e822b9da4b/GCF_014042165.1_ASM1404216v1_genomic.fna.gz --refList GCF_014042165.1_ASM1404216v1_genomic.fna/target_genomes.txt --output GCF_014042165.1_ASM1404216v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:28,259] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:28,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f872e2f-30d7-490e-8b13-5cfbe9e33440/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:28,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f872e2f-30d7-490e-8b13-5cfbe9e33440/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:28,267] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:28,267] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:28,267] [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
Moheibacter lacus	strain=BDHS18	GCA_014042165.1	2745851	2745851	type	True	100.0	920	920	95	conclusive
Moheibacter sediminis	strain=CGMCC 1.12708	GCA_900176425.1	1434700	1434700	type	True	77.8786	298	920	95	below_threshold
Empedobacter tilapiae	strain=MRS2	GCA_004785645.1	2491114	2491114	type	True	77.8246	66	920	95	below_threshold
Weeksella virosa	strain=NCTC11634	GCA_900637795.1	1014	1014	type	True	76.3481	54	920	95	below_threshold
Weeksella virosa	strain=DSM 16922	GCA_000189415.1	1014	1014	type	True	76.3143	55	920	95	below_threshold
Empedobacter brevis	strain=NBRC 14943	GCA_007990795.1	247	247	type	True	76.0304	68	920	95	below_threshold
Empedobacter brevis	strain=ATCC 43319	GCA_000382425.1	247	247	type	True	75.7815	70	920	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:28,269] [INFO] DFAST Taxonomy check result was written to GCF_014042165.1_ASM1404216v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:28,269] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:28,269] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:28,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f872e2f-30d7-490e-8b13-5cfbe9e33440/dqc_reference/checkm_data
[2024-01-24 13:28:28,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:28,298] [INFO] Task started: CheckM
[2024-01-24 13:28:28,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014042165.1_ASM1404216v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014042165.1_ASM1404216v1_genomic.fna/checkm_input GCF_014042165.1_ASM1404216v1_genomic.fna/checkm_result
[2024-01-24 13:29:11,472] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:11,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:11,493] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:11,493] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:11,493] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014042165.1_ASM1404216v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:11,494] [INFO] Task started: Blastn
[2024-01-24 13:29:11,494] [INFO] Running command: blastn -query GCF_014042165.1_ASM1404216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f872e2f-30d7-490e-8b13-5cfbe9e33440/dqc_reference/reference_markers_gtdb.fasta -out GCF_014042165.1_ASM1404216v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:12,302] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:12,305] [INFO] Selected 15 target genomes.
[2024-01-24 13:29:12,305] [INFO] Target genome list was writen to GCF_014042165.1_ASM1404216v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:12,319] [INFO] Task started: fastANI
[2024-01-24 13:29:12,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg2793d6f0-e99e-4075-957b-88e822b9da4b/GCF_014042165.1_ASM1404216v1_genomic.fna.gz --refList GCF_014042165.1_ASM1404216v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014042165.1_ASM1404216v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:19,585] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:19,593] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:19,593] [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_014042165.1	s__Moheibacter lacus	100.0	920	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Moheibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012522185.1	s__Moheibacter sp012522185	78.8843	368	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Moheibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176425.1	s__Moheibacter sediminis	77.8749	299	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Moheibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089075.1	s__Vaginella massiliensis	77.3688	64	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Vaginella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359055.1	s__UBA3376 sp002359055	76.9525	132	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__UBA3376	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142565.1	s__Chishuiella changwenlii	76.2816	52	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chishuiella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013116755.1	s__Empedobacter stercoris	76.163	61	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	99.07	99.07	0.96	0.96	2	-
GCF_000382425.1	s__Empedobacter brevis	75.8067	71	920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	98.11	96.51	0.89	0.85	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:19,594] [INFO] GTDB search result was written to GCF_014042165.1_ASM1404216v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:19,595] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:19,597] [INFO] DFAST_QC result json was written to GCF_014042165.1_ASM1404216v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:19,598] [INFO] DFAST_QC completed!
[2024-01-24 13:29:19,598] [INFO] Total running time: 0h1m19s