[2024-01-24 13:57:16,503] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:16,507] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:16,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg2513a65d-ff8e-4847-95f2-3b25c28d1639/dqc_reference
[2024-01-24 13:57:17,815] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:17,816] [INFO] Task started: Prodigal
[2024-01-24 13:57:17,816] [INFO] Running command: gunzip -c /var/lib/cwl/stgf621f409-7498-4cda-ac33-b49cd69f6812/GCF_000620085.1_ASM62008v1_genomic.fna.gz | prodigal -d GCF_000620085.1_ASM62008v1_genomic.fna/cds.fna -a GCF_000620085.1_ASM62008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:31,571] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:31,572] [INFO] Task started: HMMsearch
[2024-01-24 13:57:31,572] [INFO] Running command: hmmsearch --tblout GCF_000620085.1_ASM62008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2513a65d-ff8e-4847-95f2-3b25c28d1639/dqc_reference/reference_markers.hmm GCF_000620085.1_ASM62008v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:31,910] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:31,911] [INFO] Found 6/6 markers.
[2024-01-24 13:57:31,956] [INFO] Query marker FASTA was written to GCF_000620085.1_ASM62008v1_genomic.fna/markers.fasta
[2024-01-24 13:57:31,956] [INFO] Task started: Blastn
[2024-01-24 13:57:31,956] [INFO] Running command: blastn -query GCF_000620085.1_ASM62008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2513a65d-ff8e-4847-95f2-3b25c28d1639/dqc_reference/reference_markers.fasta -out GCF_000620085.1_ASM62008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:32,619] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:32,622] [INFO] Selected 28 target genomes.
[2024-01-24 13:57:32,622] [INFO] Target genome list was writen to GCF_000620085.1_ASM62008v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:32,630] [INFO] Task started: fastANI
[2024-01-24 13:57:32,631] [INFO] Running command: fastANI --query /var/lib/cwl/stgf621f409-7498-4cda-ac33-b49cd69f6812/GCF_000620085.1_ASM62008v1_genomic.fna.gz --refList GCF_000620085.1_ASM62008v1_genomic.fna/target_genomes.txt --output GCF_000620085.1_ASM62008v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:54,030] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:54,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2513a65d-ff8e-4847-95f2-3b25c28d1639/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:54,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2513a65d-ff8e-4847-95f2-3b25c28d1639/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:54,057] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:54,058] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:54,058] [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
Marinobacterium jannaschii	strain=DSM 6295	GCA_000620085.1	64970	64970	type	True	100.0	1706	1706	95	conclusive
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	78.3775	394	1706	95	below_threshold
Neptuniibacter caesariensis	strain=MED92	GCA_000153345.1	207954	207954	type	True	78.1379	144	1706	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	77.8801	235	1706	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	77.8442	240	1706	95	below_threshold
Neptunomonas concharum	strain=JCM 17730	GCA_006148955.1	1031538	1031538	type	True	77.536	68	1706	95	below_threshold
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	77.4975	228	1706	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	77.3946	198	1706	95	below_threshold
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	77.3818	234	1706	95	below_threshold
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	77.3107	246	1706	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	77.2865	217	1706	95	below_threshold
Marinobacterium litorale	strain=DSM 23545	GCA_000428985.1	404770	404770	type	True	77.2409	188	1706	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	77.1738	167	1706	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	77.0542	232	1706	95	below_threshold
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	77.0521	180	1706	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	76.9832	237	1706	95	below_threshold
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	76.9399	188	1706	95	below_threshold
Motiliproteus coralliicola	strain=C34	GCA_003345655.1	2283196	2283196	type	True	76.8612	206	1706	95	below_threshold
Motiliproteus sediminis	strain=HS6	GCA_017912535.1	1468178	1468178	type	True	76.5214	121	1706	95	below_threshold
Ferrimonas marina	strain=DSM 16917	GCA_900129905.1	299255	299255	type	True	76.4817	73	1706	95	below_threshold
Ferrimonas marina	strain=NBRC 102583	GCA_001571125.1	299255	299255	type	True	76.4384	72	1706	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	76.1116	60	1706	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	76.0421	64	1706	95	below_threshold
Aeromonas simiae	strain=CIP 107798	GCA_000820125.1	218936	218936	type	True	75.9652	60	1706	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	75.8624	91	1706	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	75.8074	78	1706	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	75.7904	79	1706	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:54,060] [INFO] DFAST Taxonomy check result was written to GCF_000620085.1_ASM62008v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:54,060] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:54,060] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:54,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2513a65d-ff8e-4847-95f2-3b25c28d1639/dqc_reference/checkm_data
[2024-01-24 13:57:54,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:54,111] [INFO] Task started: CheckM
[2024-01-24 13:57:54,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000620085.1_ASM62008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000620085.1_ASM62008v1_genomic.fna/checkm_input GCF_000620085.1_ASM62008v1_genomic.fna/checkm_result
[2024-01-24 13:58:36,281] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:36,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:36,301] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:36,301] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:36,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000620085.1_ASM62008v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:36,302] [INFO] Task started: Blastn
[2024-01-24 13:58:36,303] [INFO] Running command: blastn -query GCF_000620085.1_ASM62008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2513a65d-ff8e-4847-95f2-3b25c28d1639/dqc_reference/reference_markers_gtdb.fasta -out GCF_000620085.1_ASM62008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:37,252] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:37,257] [INFO] Selected 24 target genomes.
[2024-01-24 13:58:37,258] [INFO] Target genome list was writen to GCF_000620085.1_ASM62008v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:37,276] [INFO] Task started: fastANI
[2024-01-24 13:58:37,277] [INFO] Running command: fastANI --query /var/lib/cwl/stgf621f409-7498-4cda-ac33-b49cd69f6812/GCF_000620085.1_ASM62008v1_genomic.fna.gz --refList GCF_000620085.1_ASM62008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000620085.1_ASM62008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:54,576] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:54,600] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:54,601] [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_000620085.1	s__Marinobacterium_B jannaschii	100.0	1706	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015209595.1	s__Pontibacterium sp015209595	78.2416	277	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Pontibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153345.1	s__Neptuniibacter caesariensis	78.1379	144	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108065.1	s__Marinobacterium lutimaris	77.858	239	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019061305.1	s__Marinobacterium sp019061305	77.6044	187	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155945.1	s__Marinobacterium stanieri	77.5876	238	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	96.47	96.47	0.91	0.91	2	-
GCA_003250495.1	s__Marinobacterium sp003250495	77.5568	182	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017051665.1	s__Amphritea spongicola	77.489	226	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017776525.1	s__Marinobacterium alkalitolerans	77.38	199	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641945.1	s__Marinobacterium zhoushanense	77.3564	234	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001528745.1	s__Marinobacterium_A profundum	77.3106	215	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084545.1	s__Marinobacterium sp019084545	77.2992	247	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924235.1	s__Amphritea sp016924235	77.2129	177	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.30	99.30	0.95	0.95	2	-
GCF_000705555.1	s__Marinobacterium sp000705555	77.1656	194	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.11	98.11	0.90	0.90	2	-
GCF_000378045.1	s__Marinobacterium_A rhizophilum	77.0465	231	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645375.1	s__Marinobacterium_A nitratireducens	76.9801	235	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111095.1	s__Amphritea atlantica	76.935	186	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067325.1	s__Amphritea sp018067325	76.8788	103	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.51	99.51	0.92	0.92	2	-
GCF_017912535.1	s__Motiliproteus sediminis	76.4945	122	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129905.1	s__Ferrimonas marina	76.4817	73	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000820125.1	s__Aeromonas simiae	75.8992	59	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.54	96.54	0.89	0.89	2	-
GCF_002112505.1	s__Pseudomonas_E sp002112505	75.7938	106	1706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	0.99	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:54,602] [INFO] GTDB search result was written to GCF_000620085.1_ASM62008v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:54,603] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:54,607] [INFO] DFAST_QC result json was written to GCF_000620085.1_ASM62008v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:54,608] [INFO] DFAST_QC completed!
[2024-01-24 13:58:54,608] [INFO] Total running time: 0h1m38s