[2024-01-24 12:05:26,607] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:26,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:26,610] [INFO] DQC Reference Directory: /var/lib/cwl/stgb000a6b5-a946-4ff1-9825-89cb3f2fe3c1/dqc_reference
[2024-01-24 12:05:30,677] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:30,679] [INFO] Task started: Prodigal
[2024-01-24 12:05:30,679] [INFO] Running command: gunzip -c /var/lib/cwl/stgb31a11cb-c002-403c-8d80-6040c8d504d9/GCF_028657945.1_ASM2865794v1_genomic.fna.gz | prodigal -d GCF_028657945.1_ASM2865794v1_genomic.fna/cds.fna -a GCF_028657945.1_ASM2865794v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:05:48,357] [INFO] Task succeeded: Prodigal
[2024-01-24 12:05:48,357] [INFO] Task started: HMMsearch
[2024-01-24 12:05:48,357] [INFO] Running command: hmmsearch --tblout GCF_028657945.1_ASM2865794v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb000a6b5-a946-4ff1-9825-89cb3f2fe3c1/dqc_reference/reference_markers.hmm GCF_028657945.1_ASM2865794v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:05:48,699] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:05:48,700] [INFO] Found 6/6 markers.
[2024-01-24 12:05:48,753] [INFO] Query marker FASTA was written to GCF_028657945.1_ASM2865794v1_genomic.fna/markers.fasta
[2024-01-24 12:05:48,754] [INFO] Task started: Blastn
[2024-01-24 12:05:48,754] [INFO] Running command: blastn -query GCF_028657945.1_ASM2865794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb000a6b5-a946-4ff1-9825-89cb3f2fe3c1/dqc_reference/reference_markers.fasta -out GCF_028657945.1_ASM2865794v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:05:49,567] [INFO] Task succeeded: Blastn
[2024-01-24 12:05:49,572] [INFO] Selected 23 target genomes.
[2024-01-24 12:05:49,573] [INFO] Target genome list was writen to GCF_028657945.1_ASM2865794v1_genomic.fna/target_genomes.txt
[2024-01-24 12:05:49,584] [INFO] Task started: fastANI
[2024-01-24 12:05:49,584] [INFO] Running command: fastANI --query /var/lib/cwl/stgb31a11cb-c002-403c-8d80-6040c8d504d9/GCF_028657945.1_ASM2865794v1_genomic.fna.gz --refList GCF_028657945.1_ASM2865794v1_genomic.fna/target_genomes.txt --output GCF_028657945.1_ASM2865794v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:07,642] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:07,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb000a6b5-a946-4ff1-9825-89cb3f2fe3c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:07,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb000a6b5-a946-4ff1-9825-89cb3f2fe3c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:07,657] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:07,657] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:07,658] [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
Thalassomonas actiniarum	strain=A5K-106	GCA_000948975.1	485447	485447	type	True	88.2169	1743	2150	95	below_threshold
Thalassomonas viridans	strain=XOM25	GCA_000948985.1	137584	137584	type	True	84.204	1554	2150	95	below_threshold
Vibrio salinus	strain=DNF-1	GCA_021272385.1	2899784	2899784	type	True	79.954	51	2150	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	79.0168	152	2150	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.4899	58	2150	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	78.4524	101	2150	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.2805	93	2150	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	78.2332	101	2150	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	78.0319	151	2150	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.996	116	2150	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.9708	103	2150	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	77.9	144	2150	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.8297	147	2150	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.7858	119	2150	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.624	148	2150	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	75.5558	54	2150	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	75.4726	71	2150	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:07,660] [INFO] DFAST Taxonomy check result was written to GCF_028657945.1_ASM2865794v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:07,660] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:07,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:07,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb000a6b5-a946-4ff1-9825-89cb3f2fe3c1/dqc_reference/checkm_data
[2024-01-24 12:06:07,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:07,724] [INFO] Task started: CheckM
[2024-01-24 12:06:07,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028657945.1_ASM2865794v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028657945.1_ASM2865794v1_genomic.fna/checkm_input GCF_028657945.1_ASM2865794v1_genomic.fna/checkm_result
[2024-01-24 12:06:59,864] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:59,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:59,887] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:59,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:59,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028657945.1_ASM2865794v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:59,888] [INFO] Task started: Blastn
[2024-01-24 12:06:59,888] [INFO] Running command: blastn -query GCF_028657945.1_ASM2865794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb000a6b5-a946-4ff1-9825-89cb3f2fe3c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_028657945.1_ASM2865794v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:01,170] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:01,173] [INFO] Selected 20 target genomes.
[2024-01-24 12:07:01,173] [INFO] Target genome list was writen to GCF_028657945.1_ASM2865794v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:01,187] [INFO] Task started: fastANI
[2024-01-24 12:07:01,188] [INFO] Running command: fastANI --query /var/lib/cwl/stgb31a11cb-c002-403c-8d80-6040c8d504d9/GCF_028657945.1_ASM2865794v1_genomic.fna.gz --refList GCF_028657945.1_ASM2865794v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028657945.1_ASM2865794v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:16,929] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:16,948] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:07:16,948] [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_000948975.1	s__Thalassomonas actiniarum	88.2104	1745	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000948985.1	s__Thalassomonas viridans	84.2129	1554	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545765.1	s__Litorilituus sp003545765	78.7446	107	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197775.1	s__Thalassotalea_A sp007197775	78.7014	117	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439335.1	s__Litorilituus lipolyticus	78.2332	109	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104455.1	s__Cognaticolwellia chukchiensis	78.0206	151	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014656435.1	s__Thalassotalea_C marina	77.9708	103	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744155.1	s__Thalassotalea sp017744155	77.9441	139	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017168195.1	s__G2M2-11 sp017168195	77.8827	139	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__G2M2-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	77.8767	141	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014076845.1	s__Colwellia_A sp014076845	77.8722	122	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	99.15	95.49	0.95	0.86	8	-
GCF_002104475.1	s__Cognaticolwellia mytili	77.8521	146	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954355.1	s__Colwellia_A hornerae	77.652	147	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	100.00	100.00	0.99	0.99	3	-
GCF_003333305.1	s__Colwellia aromaticivorans	77.6109	122	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215385.1	s__Colwellia_A sp013215385	77.6085	134	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015491935.1	s__GCA-2401725 sp015491935	77.5886	99	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013216015.1	s__JABSOI01 sp013216015	77.4258	142	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013216005.1	s__JABSOI01 sp013216005	77.3693	119	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163005.1	s__Colwellia psychrerythraea_C	77.3326	114	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401725.1	s__GCA-2401725 sp002401725	77.3018	88	2150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:16,950] [INFO] GTDB search result was written to GCF_028657945.1_ASM2865794v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:16,951] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:16,955] [INFO] DFAST_QC result json was written to GCF_028657945.1_ASM2865794v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:16,956] [INFO] DFAST_QC completed!
[2024-01-24 12:07:16,956] [INFO] Total running time: 0h1m50s