[2024-01-24 12:46:49,513] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:49,515] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:49,515] [INFO] DQC Reference Directory: /var/lib/cwl/stg3352915a-c98b-4023-990b-c77c10e9e587/dqc_reference
[2024-01-24 12:46:50,699] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:50,700] [INFO] Task started: Prodigal
[2024-01-24 12:46:50,700] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6efbc28-1dd0-49e6-81cc-3e2d588f4c73/GCF_003449015.1_ASM344901v1_genomic.fna.gz | prodigal -d GCF_003449015.1_ASM344901v1_genomic.fna/cds.fna -a GCF_003449015.1_ASM344901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:06,329] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:06,330] [INFO] Task started: HMMsearch
[2024-01-24 12:47:06,330] [INFO] Running command: hmmsearch --tblout GCF_003449015.1_ASM344901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3352915a-c98b-4023-990b-c77c10e9e587/dqc_reference/reference_markers.hmm GCF_003449015.1_ASM344901v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:06,596] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:06,597] [INFO] Found 6/6 markers.
[2024-01-24 12:47:06,638] [INFO] Query marker FASTA was written to GCF_003449015.1_ASM344901v1_genomic.fna/markers.fasta
[2024-01-24 12:47:06,638] [INFO] Task started: Blastn
[2024-01-24 12:47:06,638] [INFO] Running command: blastn -query GCF_003449015.1_ASM344901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3352915a-c98b-4023-990b-c77c10e9e587/dqc_reference/reference_markers.fasta -out GCF_003449015.1_ASM344901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:07,260] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:07,263] [INFO] Selected 12 target genomes.
[2024-01-24 12:47:07,263] [INFO] Target genome list was writen to GCF_003449015.1_ASM344901v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:07,270] [INFO] Task started: fastANI
[2024-01-24 12:47:07,270] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6efbc28-1dd0-49e6-81cc-3e2d588f4c73/GCF_003449015.1_ASM344901v1_genomic.fna.gz --refList GCF_003449015.1_ASM344901v1_genomic.fna/target_genomes.txt --output GCF_003449015.1_ASM344901v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:16,425] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:16,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3352915a-c98b-4023-990b-c77c10e9e587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:16,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3352915a-c98b-4023-990b-c77c10e9e587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:16,436] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:16,436] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:16,436] [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
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	100.0	1681	1682	95	conclusive
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	93.7521	1376	1682	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	92.2299	1313	1682	95	below_threshold
Aureibaculum marinum	strain=BH-SD17	GCA_003813905.1	2487930	2487930	type	True	79.9829	717	1682	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	76.9011	215	1682	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	76.878	141	1682	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	76.8189	224	1682	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.7512	191	1682	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	76.6617	217	1682	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	76.5365	174	1682	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.464	175	1682	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.406	160	1682	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:16,439] [INFO] DFAST Taxonomy check result was written to GCF_003449015.1_ASM344901v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:16,439] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:16,439] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:16,440] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3352915a-c98b-4023-990b-c77c10e9e587/dqc_reference/checkm_data
[2024-01-24 12:47:16,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:16,487] [INFO] Task started: CheckM
[2024-01-24 12:47:16,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003449015.1_ASM344901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003449015.1_ASM344901v1_genomic.fna/checkm_input GCF_003449015.1_ASM344901v1_genomic.fna/checkm_result
[2024-01-24 12:48:02,911] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:02,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:02,937] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:02,937] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:02,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003449015.1_ASM344901v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:02,938] [INFO] Task started: Blastn
[2024-01-24 12:48:02,938] [INFO] Running command: blastn -query GCF_003449015.1_ASM344901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3352915a-c98b-4023-990b-c77c10e9e587/dqc_reference/reference_markers_gtdb.fasta -out GCF_003449015.1_ASM344901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:03,864] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:03,867] [INFO] Selected 9 target genomes.
[2024-01-24 12:48:03,868] [INFO] Target genome list was writen to GCF_003449015.1_ASM344901v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:03,878] [INFO] Task started: fastANI
[2024-01-24 12:48:03,878] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6efbc28-1dd0-49e6-81cc-3e2d588f4c73/GCF_003449015.1_ASM344901v1_genomic.fna.gz --refList GCF_003449015.1_ASM344901v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003449015.1_ASM344901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:11,395] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:11,404] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:11,404] [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_003449015.1	s__Aureibaculum sp003449015	100.0	1681	1682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_006065315.1	s__Aureibaculum sp006065315	93.74	1377	1682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406085.1	s__Aureibaculum sp016406085	92.2299	1313	1682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003813905.1	s__Aureibaculum marinum	79.983	717	1682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511845.1	s__Aureibaculum sp003511845	78.1483	248	1682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	99.43	99.43	0.80	0.80	2	-
GCA_002352665.1	s__Aureibaculum sp002352665	77.9625	399	1682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	76.9128	214	1682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	76.6353	191	1682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195315.1	s__Lutibacter sp004195315	76.4617	138	1682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:11,405] [INFO] GTDB search result was written to GCF_003449015.1_ASM344901v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:11,406] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:11,409] [INFO] DFAST_QC result json was written to GCF_003449015.1_ASM344901v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:11,409] [INFO] DFAST_QC completed!
[2024-01-24 12:48:11,409] [INFO] Total running time: 0h1m22s