[2024-01-24 13:46:10,997] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:10,999] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:10,999] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5f6d2e5-43da-47bf-97e9-d505e611ea3f/dqc_reference
[2024-01-24 13:46:12,443] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:12,444] [INFO] Task started: Prodigal
[2024-01-24 13:46:12,444] [INFO] Running command: gunzip -c /var/lib/cwl/stg34e2c2cf-1de0-4d46-a909-d2bbc91c4d4c/GCF_008973755.1_ASM897375v1_genomic.fna.gz | prodigal -d GCF_008973755.1_ASM897375v1_genomic.fna/cds.fna -a GCF_008973755.1_ASM897375v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:24,591] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:24,592] [INFO] Task started: HMMsearch
[2024-01-24 13:46:24,592] [INFO] Running command: hmmsearch --tblout GCF_008973755.1_ASM897375v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5f6d2e5-43da-47bf-97e9-d505e611ea3f/dqc_reference/reference_markers.hmm GCF_008973755.1_ASM897375v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:24,940] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:24,942] [INFO] Found 6/6 markers.
[2024-01-24 13:46:25,000] [INFO] Query marker FASTA was written to GCF_008973755.1_ASM897375v1_genomic.fna/markers.fasta
[2024-01-24 13:46:25,001] [INFO] Task started: Blastn
[2024-01-24 13:46:25,001] [INFO] Running command: blastn -query GCF_008973755.1_ASM897375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5f6d2e5-43da-47bf-97e9-d505e611ea3f/dqc_reference/reference_markers.fasta -out GCF_008973755.1_ASM897375v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:25,823] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:25,827] [INFO] Selected 28 target genomes.
[2024-01-24 13:46:25,827] [INFO] Target genome list was writen to GCF_008973755.1_ASM897375v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:25,849] [INFO] Task started: fastANI
[2024-01-24 13:46:25,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg34e2c2cf-1de0-4d46-a909-d2bbc91c4d4c/GCF_008973755.1_ASM897375v1_genomic.fna.gz --refList GCF_008973755.1_ASM897375v1_genomic.fna/target_genomes.txt --output GCF_008973755.1_ASM897375v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:49,881] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:49,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5f6d2e5-43da-47bf-97e9-d505e611ea3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:49,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5f6d2e5-43da-47bf-97e9-d505e611ea3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:49,904] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:49,904] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:49,904] [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
Nitrincola alkalilacustris	strain=NCAIM B.02612	GCA_008973755.1	1571224	1571224	type	True	100.0	1342	1342	95	conclusive
Nitrincola schmidtii	strain=NCAIM B.02626	GCA_008973715.1	1730894	1730894	type	True	77.9794	112	1342	95	below_threshold
Nitrincola lacisaponensis	strain=4CA	GCA_000691225.1	267850	267850	type	True	77.7423	204	1342	95	below_threshold
Nitrincola iocasae	strain=KXZD1103	GCA_008727795.1	2614693	2614693	type	True	77.6642	198	1342	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	77.6616	179	1342	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	77.6283	170	1342	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	77.5413	187	1342	95	below_threshold
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	77.4832	179	1342	95	below_threshold
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	77.4829	203	1342	95	below_threshold
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	77.4594	197	1342	95	below_threshold
Marinobacterium litorale	strain=DSM 23545	GCA_000428985.1	404770	404770	type	True	77.4191	135	1342	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	77.4162	170	1342	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	77.3598	159	1342	95	below_threshold
Neptuniibacter caesariensis	strain=MED92	GCA_000153345.1	207954	207954	type	True	76.9353	57	1342	95	below_threshold
Marinobacterium jannaschii	strain=DSM 6295	GCA_000620085.1	64970	64970	type	True	76.8871	135	1342	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	76.5363	61	1342	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	76.4752	66	1342	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	76.3438	68	1342	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	76.1821	66	1342	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	76.16	68	1342	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	76.015	59	1342	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:49,906] [INFO] DFAST Taxonomy check result was written to GCF_008973755.1_ASM897375v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:49,907] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:49,907] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:49,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5f6d2e5-43da-47bf-97e9-d505e611ea3f/dqc_reference/checkm_data
[2024-01-24 13:46:49,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:49,957] [INFO] Task started: CheckM
[2024-01-24 13:46:49,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008973755.1_ASM897375v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008973755.1_ASM897375v1_genomic.fna/checkm_input GCF_008973755.1_ASM897375v1_genomic.fna/checkm_result
[2024-01-24 13:47:30,112] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:30,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:30,132] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:30,132] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:30,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008973755.1_ASM897375v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:30,133] [INFO] Task started: Blastn
[2024-01-24 13:47:30,133] [INFO] Running command: blastn -query GCF_008973755.1_ASM897375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5f6d2e5-43da-47bf-97e9-d505e611ea3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_008973755.1_ASM897375v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:31,033] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:31,036] [INFO] Selected 25 target genomes.
[2024-01-24 13:47:31,036] [INFO] Target genome list was writen to GCF_008973755.1_ASM897375v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:31,064] [INFO] Task started: fastANI
[2024-01-24 13:47:31,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg34e2c2cf-1de0-4d46-a909-d2bbc91c4d4c/GCF_008973755.1_ASM897375v1_genomic.fna.gz --refList GCF_008973755.1_ASM897375v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008973755.1_ASM897375v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:47,220] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:47,245] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:47,246] [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_008973755.1	s__Nitrincola alkalilacustris	100.0	1342	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000764495.1	s__Nitrincola sp000764495	78.202	168	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008368715.1	s__Nitrincola tapanii	78.0255	128	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000691225.1	s__Nitrincola lacisaponensis	77.7578	203	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727795.1	s__Nitrincola sp008727795	77.6643	198	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019061305.1	s__Marinobacterium sp019061305	77.6542	166	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017776525.1	s__Marinobacterium alkalitolerans	77.6442	180	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014615.1	s__Marinobacterium halophilum	77.5362	185	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.87	98.87	0.91	0.91	2	-
GCF_900155945.1	s__Marinobacterium stanieri	77.4832	179	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	96.47	96.47	0.91	0.91	2	-
GCF_019084545.1	s__Marinobacterium sp019084545	77.4568	203	1342	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	77.4359	197	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428985.1	s__Marinobacterium litorale	77.4302	133	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	97.80	97.80	0.87	0.87	2	-
GCF_900108065.1	s__Marinobacterium lutimaris	77.4069	169	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339595.1	s__Marinobacterium mangrovicola	77.3598	159	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000705555.1	s__Marinobacterium sp000705555	77.2747	176	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.11	98.11	0.90	0.90	2	-
GCA_003250495.1	s__Marinobacterium sp003250495	77.1524	137	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209595.1	s__Pontibacterium sp015209595	77.1263	94	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Pontibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744735.1	s__Marinobacter guineae	76.5363	61	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686085.1	s__Marinobacter sp000686085	76.348	70	1342	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:47,247] [INFO] GTDB search result was written to GCF_008973755.1_ASM897375v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:47,248] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:47,253] [INFO] DFAST_QC result json was written to GCF_008973755.1_ASM897375v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:47,253] [INFO] DFAST_QC completed!
[2024-01-24 13:47:47,253] [INFO] Total running time: 0h1m36s