[2023-06-28 00:14:07,036] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:14:07,039] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:14:07,039] [INFO] DQC Reference Directory: /var/lib/cwl/stg732ed95c-f601-4251-bc55-57855a34150b/dqc_reference
[2023-06-28 00:14:08,338] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:14:08,339] [INFO] Task started: Prodigal
[2023-06-28 00:14:08,339] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c69f244-0fe8-4138-b221-59d397d05d17/GCA_026708635.1_ASM2670863v1_genomic.fna.gz | prodigal -d GCA_026708635.1_ASM2670863v1_genomic.fna/cds.fna -a GCA_026708635.1_ASM2670863v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:14:17,002] [INFO] Task succeeded: Prodigal
[2023-06-28 00:14:17,003] [INFO] Task started: HMMsearch
[2023-06-28 00:14:17,003] [INFO] Running command: hmmsearch --tblout GCA_026708635.1_ASM2670863v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg732ed95c-f601-4251-bc55-57855a34150b/dqc_reference/reference_markers.hmm GCA_026708635.1_ASM2670863v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:14:17,261] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:14:17,263] [INFO] Found 6/6 markers.
[2023-06-28 00:14:17,297] [INFO] Query marker FASTA was written to GCA_026708635.1_ASM2670863v1_genomic.fna/markers.fasta
[2023-06-28 00:14:17,298] [INFO] Task started: Blastn
[2023-06-28 00:14:17,298] [INFO] Running command: blastn -query GCA_026708635.1_ASM2670863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg732ed95c-f601-4251-bc55-57855a34150b/dqc_reference/reference_markers.fasta -out GCA_026708635.1_ASM2670863v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:14:17,948] [INFO] Task succeeded: Blastn
[2023-06-28 00:14:17,953] [INFO] Selected 29 target genomes.
[2023-06-28 00:14:17,954] [INFO] Target genome list was writen to GCA_026708635.1_ASM2670863v1_genomic.fna/target_genomes.txt
[2023-06-28 00:14:17,983] [INFO] Task started: fastANI
[2023-06-28 00:14:17,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c69f244-0fe8-4138-b221-59d397d05d17/GCA_026708635.1_ASM2670863v1_genomic.fna.gz --refList GCA_026708635.1_ASM2670863v1_genomic.fna/target_genomes.txt --output GCA_026708635.1_ASM2670863v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:14:36,971] [INFO] Task succeeded: fastANI
[2023-06-28 00:14:36,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg732ed95c-f601-4251-bc55-57855a34150b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:14:36,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg732ed95c-f601-4251-bc55-57855a34150b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:14:36,990] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:14:36,990] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 00:14:36,991] [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
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	76.4776	77	1003	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	76.3686	86	1003	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	76.3109	104	1003	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	76.1852	99	1003	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	76.1744	94	1003	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.1136	70	1003	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	76.0772	95	1003	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	76.0499	92	1003	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.0366	76	1003	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	75.9936	95	1003	95	below_threshold
Paracoccus denitrificans	strain=DSM 413	GCA_900100045.1	266	266	type	True	75.9176	85	1003	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	75.9008	66	1003	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	75.8981	84	1003	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	75.8976	54	1003	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	75.8952	94	1003	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	75.894	95	1003	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	75.8893	93	1003	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	75.8817	91	1003	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	75.8796	84	1003	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	75.7818	76	1003	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	75.6974	85	1003	95	below_threshold
Amaricoccus macauensis	strain=DSM 101730	GCA_014201905.1	57001	57001	type	True	75.6796	54	1003	95	below_threshold
Defluviimonas aquaemixtae	strain=CECT 8626	GCA_900302475.1	1542388	1542388	type	True	75.6374	77	1003	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	75.5593	79	1003	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	75.559	77	1003	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 00:14:36,993] [INFO] DFAST Taxonomy check result was written to GCA_026708635.1_ASM2670863v1_genomic.fna/tc_result.tsv
[2023-06-28 00:14:36,994] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:14:36,994] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:14:36,994] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg732ed95c-f601-4251-bc55-57855a34150b/dqc_reference/checkm_data
[2023-06-28 00:14:36,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:14:37,032] [INFO] Task started: CheckM
[2023-06-28 00:14:37,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708635.1_ASM2670863v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708635.1_ASM2670863v1_genomic.fna/checkm_input GCA_026708635.1_ASM2670863v1_genomic.fna/checkm_result
[2023-06-28 00:15:07,627] [INFO] Task succeeded: CheckM
[2023-06-28 00:15:07,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:15:07,654] [INFO] ===== Completeness check finished =====
[2023-06-28 00:15:07,654] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:15:07,655] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708635.1_ASM2670863v1_genomic.fna/markers.fasta)
[2023-06-28 00:15:07,655] [INFO] Task started: Blastn
[2023-06-28 00:15:07,655] [INFO] Running command: blastn -query GCA_026708635.1_ASM2670863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg732ed95c-f601-4251-bc55-57855a34150b/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708635.1_ASM2670863v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:15:08,636] [INFO] Task succeeded: Blastn
[2023-06-28 00:15:08,640] [INFO] Selected 33 target genomes.
[2023-06-28 00:15:08,640] [INFO] Target genome list was writen to GCA_026708635.1_ASM2670863v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:15:08,689] [INFO] Task started: fastANI
[2023-06-28 00:15:08,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c69f244-0fe8-4138-b221-59d397d05d17/GCA_026708635.1_ASM2670863v1_genomic.fna.gz --refList GCA_026708635.1_ASM2670863v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708635.1_ASM2670863v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:15:29,540] [INFO] Task succeeded: fastANI
[2023-06-28 00:15:29,569] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 00:15:29,569] [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_003129565.1	s__Salibaculum griseiflavum	76.4776	77	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	76.3943	85	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	76.3686	86	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_009363255.1	s__Roseivivax sp009363255	76.362	72	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	99.55	99.55	0.94	0.94	2	-
GCF_004343075.1	s__Rhodovulum marinum	76.3273	103	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	76.2838	114	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	76.2621	93	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	76.192	93	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	76.1852	99	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	76.1702	65	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	76.1396	106	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	76.1245	104	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	76.0366	76	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_003344785.1	s__Puniceibacterium profundi	76.0255	90	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002751875.1	s__Oceaniglobus indicus	75.9797	68	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	75.9735	104	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100045.1	s__Paracoccus denitrificans	75.9352	84	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	-
GCF_000379485.1	s__Wenxinia marina	75.9215	91	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_000521865.1	s__Roseivivax isoporae	75.8921	94	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111685.1	s__Salipiger pacificus_A	75.8845	93	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_002300555.1	s__Salipiger sp002300555	75.8722	80	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046725.1	s__DSPG01 sp011046725	75.8016	81	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DSPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458395.1	s__Leisingera aquaemixtae	75.7891	73	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_000299575.1	s__Palleronia guishaninsula	75.7225	70	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014903745.1	s__Mangrovicoccus sp014903745	75.7086	84	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009835145.1	s__Profundibacterium mesophilum	75.6773	83	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	75.6752	100	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003500165.1	s__UBA10424 sp003500165	75.6163	91	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA10424	95.0	99.72	99.62	0.98	0.98	3	-
GCF_004000435.1	s__Flavimaricola sp004000435	75.559	77	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	99.99	99.97	0.99	0.98	36	-
--------------------------------------------------------------------------------
[2023-06-28 00:15:29,571] [INFO] GTDB search result was written to GCA_026708635.1_ASM2670863v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:15:29,572] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:15:29,577] [INFO] DFAST_QC result json was written to GCA_026708635.1_ASM2670863v1_genomic.fna/dqc_result.json
[2023-06-28 00:15:29,577] [INFO] DFAST_QC completed!
[2023-06-28 00:15:29,578] [INFO] Total running time: 0h1m23s