[2024-01-24 12:13:28,846] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,849] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,849] [INFO] DQC Reference Directory: /var/lib/cwl/stg38993800-3e47-4276-9023-49f8eeee6272/dqc_reference
[2024-01-24 12:13:30,226] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,227] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,227] [INFO] Running command: gunzip -c /var/lib/cwl/stgd99db3cd-a2d1-46d1-b0fd-03b6f3829748/GCF_030295975.1_ASM3029597v1_genomic.fna.gz | prodigal -d GCF_030295975.1_ASM3029597v1_genomic.fna/cds.fna -a GCF_030295975.1_ASM3029597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:39,818] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:39,818] [INFO] Task started: HMMsearch
[2024-01-24 12:13:39,819] [INFO] Running command: hmmsearch --tblout GCF_030295975.1_ASM3029597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38993800-3e47-4276-9023-49f8eeee6272/dqc_reference/reference_markers.hmm GCF_030295975.1_ASM3029597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:40,231] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:40,236] [INFO] Found 6/6 markers.
[2024-01-24 12:13:40,283] [INFO] Query marker FASTA was written to GCF_030295975.1_ASM3029597v1_genomic.fna/markers.fasta
[2024-01-24 12:13:40,283] [INFO] Task started: Blastn
[2024-01-24 12:13:40,283] [INFO] Running command: blastn -query GCF_030295975.1_ASM3029597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38993800-3e47-4276-9023-49f8eeee6272/dqc_reference/reference_markers.fasta -out GCF_030295975.1_ASM3029597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:41,050] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:41,054] [INFO] Selected 25 target genomes.
[2024-01-24 12:13:41,054] [INFO] Target genome list was writen to GCF_030295975.1_ASM3029597v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:41,062] [INFO] Task started: fastANI
[2024-01-24 12:13:41,062] [INFO] Running command: fastANI --query /var/lib/cwl/stgd99db3cd-a2d1-46d1-b0fd-03b6f3829748/GCF_030295975.1_ASM3029597v1_genomic.fna.gz --refList GCF_030295975.1_ASM3029597v1_genomic.fna/target_genomes.txt --output GCF_030295975.1_ASM3029597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:00,711] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:00,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38993800-3e47-4276-9023-49f8eeee6272/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:00,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38993800-3e47-4276-9023-49f8eeee6272/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:00,726] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:14:00,726] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:14:00,726] [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
Thalassotalea crassostreae	strain=LPB0090	GCA_001831495.1	1763536	1763536	type	True	79.0383	136	1462	95	below_threshold
Vibrio echinoideorum	strain=DSM 107264	GCA_024347455.1	2100116	2100116	type	True	78.9216	52	1462	95	below_threshold
Vibrio gallaecicus	strain=CECT 7244	GCA_024347495.1	552386	552386	type	True	78.8611	58	1462	95	below_threshold
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	78.6505	269	1462	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.6332	201	1462	95	below_threshold
Moritella yayanosii	strain=DB21MT 5	GCA_900465055.1	69539	69539	type	True	78.5403	57	1462	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	78.5007	177	1462	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	78.1981	130	1462	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001652445.1	1763536	1763536	type	True	78.1704	128	1462	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.0346	226	1462	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.9759	160	1462	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.9592	159	1462	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.939	172	1462	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.9063	165	1462	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.7563	171	1462	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.7112	187	1462	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.6445	202	1462	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	77.3659	82	1462	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:00,728] [INFO] DFAST Taxonomy check result was written to GCF_030295975.1_ASM3029597v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:00,729] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:00,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:00,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38993800-3e47-4276-9023-49f8eeee6272/dqc_reference/checkm_data
[2024-01-24 12:14:00,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:00,772] [INFO] Task started: CheckM
[2024-01-24 12:14:00,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030295975.1_ASM3029597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030295975.1_ASM3029597v1_genomic.fna/checkm_input GCF_030295975.1_ASM3029597v1_genomic.fna/checkm_result
[2024-01-24 12:14:36,036] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:36,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:36,060] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:36,060] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:36,061] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030295975.1_ASM3029597v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:36,061] [INFO] Task started: Blastn
[2024-01-24 12:14:36,061] [INFO] Running command: blastn -query GCF_030295975.1_ASM3029597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38993800-3e47-4276-9023-49f8eeee6272/dqc_reference/reference_markers_gtdb.fasta -out GCF_030295975.1_ASM3029597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:37,264] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:37,268] [INFO] Selected 25 target genomes.
[2024-01-24 12:14:37,269] [INFO] Target genome list was writen to GCF_030295975.1_ASM3029597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:37,286] [INFO] Task started: fastANI
[2024-01-24 12:14:37,286] [INFO] Running command: fastANI --query /var/lib/cwl/stgd99db3cd-a2d1-46d1-b0fd-03b6f3829748/GCF_030295975.1_ASM3029597v1_genomic.fna.gz --refList GCF_030295975.1_ASM3029597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030295975.1_ASM3029597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:55,755] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:55,772] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:14:55,772] [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_001831495.1	s__Thalassotalea_A crassostreae	78.9842	136	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004295665.1	s__Litorilituus sediminis	78.7816	202	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390375.1	s__Thalassotalea euphylliae_A	78.7605	228	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	78.6341	229	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932965.1	s__Thalassotalea algicola	78.6233	270	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390335.1	s__Thalassotalea euphylliae_B	78.5578	213	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002077175.1	s__Cognaticolwellia sp002077175	78.4894	214	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002076895.1	s__Cognaticolwellia beringensis	78.4173	202	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390395.1	s__Thalassotalea euphylliae_C	78.4023	247	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	78.3092	185	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744155.1	s__Thalassotalea sp017744155	78.2573	154	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077005.1	s__Cognaticolwellia sp014077005	78.161	180	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	78.1561	198	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002162925.1	s__Thalassotalea_A sp002162925	78.0893	116	1462	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_002104475.1	s__Cognaticolwellia mytili	78.0583	227	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843355.2	s__Colwellia echini	77.9646	163	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378625.1	s__Colwellia piezophila	77.7599	171	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003545415.1	s__Colwellia sp003545415	77.6429	141	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013216015.1	s__JABSOI01 sp013216015	77.5231	157	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	77.2135	213	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:55,774] [INFO] GTDB search result was written to GCF_030295975.1_ASM3029597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:55,774] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:55,779] [INFO] DFAST_QC result json was written to GCF_030295975.1_ASM3029597v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:55,779] [INFO] DFAST_QC completed!
[2024-01-24 12:14:55,779] [INFO] Total running time: 0h1m27s