[2023-03-18 07:54:30,541] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:54:30,542] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:54:30,542] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7845cbc-ee67-4ef9-a91f-bc3eef1c6b80/dqc_reference
[2023-03-18 07:54:32,271] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:54:32,271] [INFO] Task started: Prodigal
[2023-03-18 07:54:32,271] [INFO] Running command: cat /var/lib/cwl/stg59d11503-f4aa-48d8-a93e-952750bda885/OceanDNA-b29544.fa | prodigal -d OceanDNA-b29544/cds.fna -a OceanDNA-b29544/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:54:41,334] [INFO] Task succeeded: Prodigal
[2023-03-18 07:54:41,335] [INFO] Task started: HMMsearch
[2023-03-18 07:54:41,335] [INFO] Running command: hmmsearch --tblout OceanDNA-b29544/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7845cbc-ee67-4ef9-a91f-bc3eef1c6b80/dqc_reference/reference_markers.hmm OceanDNA-b29544/protein.faa > /dev/null
[2023-03-18 07:54:41,498] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:54:41,498] [INFO] Found 6/6 markers.
[2023-03-18 07:54:41,510] [INFO] Query marker FASTA was written to OceanDNA-b29544/markers.fasta
[2023-03-18 07:54:41,512] [INFO] Task started: Blastn
[2023-03-18 07:54:41,512] [INFO] Running command: blastn -query OceanDNA-b29544/markers.fasta -db /var/lib/cwl/stgc7845cbc-ee67-4ef9-a91f-bc3eef1c6b80/dqc_reference/reference_markers.fasta -out OceanDNA-b29544/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:54:42,350] [INFO] Task succeeded: Blastn
[2023-03-18 07:54:42,351] [INFO] Selected 27 target genomes.
[2023-03-18 07:54:42,351] [INFO] Target genome list was writen to OceanDNA-b29544/target_genomes.txt
[2023-03-18 07:54:42,367] [INFO] Task started: fastANI
[2023-03-18 07:54:42,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg59d11503-f4aa-48d8-a93e-952750bda885/OceanDNA-b29544.fa --refList OceanDNA-b29544/target_genomes.txt --output OceanDNA-b29544/fastani_result.tsv --threads 1
[2023-03-18 07:54:59,488] [INFO] Task succeeded: fastANI
[2023-03-18 07:54:59,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7845cbc-ee67-4ef9-a91f-bc3eef1c6b80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:54:59,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7845cbc-ee67-4ef9-a91f-bc3eef1c6b80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:54:59,502] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:54:59,503] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:54:59,503] [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
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	78.9994	212	485	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.9434	225	485	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	78.8595	228	485	95	below_threshold
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	78.7143	204	485	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.7022	242	485	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.6073	212	485	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	78.5956	219	485	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.4818	209	485	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	78.3722	184	485	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.2195	217	485	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.2084	217	485	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.2	220	485	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.1947	212	485	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.1593	181	485	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	78.1268	167	485	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.1172	200	485	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.1145	198	485	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	78.1063	189	485	95	below_threshold
Thioclava marina	strain=11.10-0-13	GCA_002020135.1	1915077	1915077	type	True	78.0892	202	485	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	78.0707	208	485	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	77.908	162	485	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	77.8135	153	485	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	77.8066	153	485	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.8003	199	485	95	below_threshold
Alkalilacustris brevis	strain=34079	GCA_003350345.1	2026338	2026338	type	True	77.5796	168	485	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	77.5281	137	485	95	below_threshold
Rubellimicrobium mesophilum	strain=DSM 19309	GCA_000600335.2	1123067	1123067	type	True	77.392	169	485	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:54:59,503] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29544/tc_result.tsv
[2023-03-18 07:54:59,503] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:54:59,503] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:54:59,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7845cbc-ee67-4ef9-a91f-bc3eef1c6b80/dqc_reference/checkm_data
[2023-03-18 07:54:59,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:54:59,514] [INFO] Task started: CheckM
[2023-03-18 07:54:59,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29544/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29544/checkm_input OceanDNA-b29544/checkm_result
[2023-03-18 07:55:26,365] [INFO] Task succeeded: CheckM
[2023-03-18 07:55:26,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:55:26,368] [INFO] ===== Completeness check finished =====
[2023-03-18 07:55:26,368] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:55:26,368] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29544/markers.fasta)
[2023-03-18 07:55:26,368] [INFO] Task started: Blastn
[2023-03-18 07:55:26,368] [INFO] Running command: blastn -query OceanDNA-b29544/markers.fasta -db /var/lib/cwl/stgc7845cbc-ee67-4ef9-a91f-bc3eef1c6b80/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29544/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:55:27,818] [INFO] Task succeeded: Blastn
[2023-03-18 07:55:27,818] [INFO] Selected 26 target genomes.
[2023-03-18 07:55:27,819] [INFO] Target genome list was writen to OceanDNA-b29544/target_genomes_gtdb.txt
[2023-03-18 07:55:27,850] [INFO] Task started: fastANI
[2023-03-18 07:55:27,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg59d11503-f4aa-48d8-a93e-952750bda885/OceanDNA-b29544.fa --refList OceanDNA-b29544/target_genomes_gtdb.txt --output OceanDNA-b29544/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:55:43,865] [INFO] Task succeeded: fastANI
[2023-03-18 07:55:43,880] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:55:43,880] [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
GCA_009920775.1	s__Marivivens sp009920775	94.3333	378	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145845.1	s__Marivivens sp004145845	79.25	252	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195545.1	s__Limimaricola variabilis	78.9994	212	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	78.9696	233	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600975.2	s__Limimaricola hongkongensis	78.8878	226	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000466965.1	s__Limimaricola cinnabarinus	78.7453	202	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	78.7202	241	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125575.1	s__JAACUH01 sp016125575	78.7176	251	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	78.5451	252	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	78.4818	209	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	78.4332	159	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	78.4148	219	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	78.2287	211	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973535.1	s__Albidovulum denitrificans	78.1972	215	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177545.1	s__Muriiphilus sp900177545	78.1841	170	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650895.1	s__EhC02 sp001650895	78.1432	198	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142295.1	s__Vannielia litorea	78.1252	210	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	78.0096	215	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115805.1	s__Marivita geojedonensis	77.8054	154	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017792425.1	s__Thalassobius sp017792425	77.7642	178	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643905.1	s__Marivita sp017643905	77.6897	143	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	77.6803	185	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018200035.1	s__Sulfitobacter sp018200035	77.6062	160	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350345.1	s__Rhodobaculum breve	77.5796	168	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115725.1	s__Marivita cryptomonadis	77.5449	137	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	99.81	99.78	0.91	0.91	31	-
GCF_000600335.2	s__Rubellimicrobium mesophilum	77.3928	169	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:55:43,880] [INFO] GTDB search result was written to OceanDNA-b29544/result_gtdb.tsv
[2023-03-18 07:55:43,880] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:55:43,883] [INFO] DFAST_QC result json was written to OceanDNA-b29544/dqc_result.json
[2023-03-18 07:55:43,883] [INFO] DFAST_QC completed!
[2023-03-18 07:55:43,883] [INFO] Total running time: 0h1m13s