[2023-03-16 18:07:32,284] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:07:32,284] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:07:32,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f7de24a-3999-4183-b826-d31516639781/dqc_reference
[2023-03-16 18:07:34,914] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:07:34,915] [INFO] Task started: Prodigal
[2023-03-16 18:07:34,916] [INFO] Running command: cat /var/lib/cwl/stg76cced33-2dc5-4443-990f-d463f475495e/OceanDNA-b27562.fa | prodigal -d OceanDNA-b27562/cds.fna -a OceanDNA-b27562/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:07:52,832] [INFO] Task succeeded: Prodigal
[2023-03-16 18:07:52,833] [INFO] Task started: HMMsearch
[2023-03-16 18:07:52,833] [INFO] Running command: hmmsearch --tblout OceanDNA-b27562/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f7de24a-3999-4183-b826-d31516639781/dqc_reference/reference_markers.hmm OceanDNA-b27562/protein.faa > /dev/null
[2023-03-16 18:07:53,022] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:07:53,022] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg76cced33-2dc5-4443-990f-d463f475495e/OceanDNA-b27562.fa]
[2023-03-16 18:07:53,042] [INFO] Query marker FASTA was written to OceanDNA-b27562/markers.fasta
[2023-03-16 18:07:53,043] [INFO] Task started: Blastn
[2023-03-16 18:07:53,043] [INFO] Running command: blastn -query OceanDNA-b27562/markers.fasta -db /var/lib/cwl/stg5f7de24a-3999-4183-b826-d31516639781/dqc_reference/reference_markers.fasta -out OceanDNA-b27562/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:07:53,766] [INFO] Task succeeded: Blastn
[2023-03-16 18:07:53,767] [INFO] Selected 29 target genomes.
[2023-03-16 18:07:53,767] [INFO] Target genome list was writen to OceanDNA-b27562/target_genomes.txt
[2023-03-16 18:07:53,842] [INFO] Task started: fastANI
[2023-03-16 18:07:53,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg76cced33-2dc5-4443-990f-d463f475495e/OceanDNA-b27562.fa --refList OceanDNA-b27562/target_genomes.txt --output OceanDNA-b27562/fastani_result.tsv --threads 1
[2023-03-16 18:08:10,772] [INFO] Task succeeded: fastANI
[2023-03-16 18:08:10,772] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f7de24a-3999-4183-b826-d31516639781/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:08:10,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f7de24a-3999-4183-b826-d31516639781/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:08:10,788] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:08:10,788] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:08:10,788] [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
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.4306	184	816	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.7542	127	816	95	below_threshold
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	76.7291	144	816	95	below_threshold
Roseovarius aestuariivivens	strain=GHTF-24	GCA_004761875.1	1888910	1888910	type	True	76.7131	110	816	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	76.706	142	816	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	76.6832	126	816	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	76.6682	125	816	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	76.6284	94	816	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001404195.1	481446	481446	type	True	76.6283	94	816	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	76.602	118	816	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	76.601	92	816	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	76.5979	94	816	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	76.5571	137	816	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	76.5413	102	816	95	below_threshold
Ruegeria conchae	strain=DSM 29317	GCA_003664205.1	981384	981384	suspected-type	True	76.5007	80	816	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	76.4962	124	816	95	below_threshold
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	76.4792	134	816	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	76.4736	123	816	95	below_threshold
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	76.4698	81	816	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.4589	132	816	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	76.368	127	816	95	below_threshold
Rubellimicrobium mesophilum	strain=DSM 19309	GCA_000600335.2	1123067	1123067	type	True	76.354	74	816	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	76.3469	124	816	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.3439	83	816	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.1562	118	816	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.138	102	816	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.1304	121	816	95	below_threshold
Donghicola eburneus	strain=DSM 29127	GCA_900115865.1	393278	393278	type	True	76.1079	80	816	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.779	75	816	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:08:10,789] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27562/tc_result.tsv
[2023-03-16 18:08:10,789] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:08:10,789] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:08:10,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f7de24a-3999-4183-b826-d31516639781/dqc_reference/checkm_data
[2023-03-16 18:08:10,790] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:08:10,795] [INFO] Task started: CheckM
[2023-03-16 18:08:10,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27562/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27562/checkm_input OceanDNA-b27562/checkm_result
[2023-03-16 18:09:01,521] [INFO] Task succeeded: CheckM
[2023-03-16 18:09:01,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:09:01,525] [INFO] ===== Completeness check finished =====
[2023-03-16 18:09:01,525] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:09:01,525] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27562/markers.fasta)
[2023-03-16 18:09:01,527] [INFO] Task started: Blastn
[2023-03-16 18:09:01,527] [INFO] Running command: blastn -query OceanDNA-b27562/markers.fasta -db /var/lib/cwl/stg5f7de24a-3999-4183-b826-d31516639781/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27562/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:09:04,628] [INFO] Task succeeded: Blastn
[2023-03-16 18:09:04,629] [INFO] Selected 29 target genomes.
[2023-03-16 18:09:04,629] [INFO] Target genome list was writen to OceanDNA-b27562/target_genomes_gtdb.txt
[2023-03-16 18:09:04,669] [INFO] Task started: fastANI
[2023-03-16 18:09:04,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg76cced33-2dc5-4443-990f-d463f475495e/OceanDNA-b27562.fa --refList OceanDNA-b27562/target_genomes_gtdb.txt --output OceanDNA-b27562/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:09:25,259] [INFO] Task succeeded: fastANI
[2023-03-16 18:09:25,275] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:09:25,275] [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_009830125.1	s__GH1-50 sp009830125	77.4306	184	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042605.1	s__IMCC34051 sp013042605	77.0071	170	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	99.10	98.86	0.88	0.86	4	-
GCA_013003075.1	s__IMCC34051 sp013003075	76.9944	114	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	76.9134	151	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762635.1	s__JABURR01 sp014762635	76.7664	151	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABURR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643905.1	s__Marivita sp017643905	76.761	125	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141995.1	s__Palleronia salina	76.744	143	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	76.706	142	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	76.6983	162	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	76.6759	128	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	76.6732	155	816	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_002285435.1	s__Actibacterium ureilyticum	76.6552	163	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	76.6291	168	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	76.602	118	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_017356265.1	s__Paracoccus fontiphilus	76.601	92	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434965.1	s__Marimonas lutisalis	76.597	125	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110115.1	s__Palleronia pelagia	76.5715	136	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_003148765.1	s__Silicimonas algicola	76.5045	121	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Silicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002869745.1	s__Oceaniglobus roseus	76.5026	142	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003605175.1	s__IMCC34051 sp003605175	76.4949	142	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768315.1	s__Pseudooceanicola atlanticus	76.4626	133	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_002073975.1	s__Rhodovulum sp002073975	76.4326	107	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813965.1	s__Leisingera sp000813965	76.4181	110	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169415.1	s__Sagittula stellata	76.4175	114	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920775.1	s__Marivivens sp009920775	76.3253	88	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708925.1	s__Thalassobius sp002708925	76.2582	93	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
GCA_018401465.1	s__Aestuariivita sp018401465	76.2383	143	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240425.1	s__TMP-24 sp018240425	76.1904	104	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__TMP-24	95.0	99.95	99.95	0.97	0.97	2	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	76.022	130	816	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:09:25,276] [INFO] GTDB search result was written to OceanDNA-b27562/result_gtdb.tsv
[2023-03-16 18:09:25,276] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:09:25,279] [INFO] DFAST_QC result json was written to OceanDNA-b27562/dqc_result.json
[2023-03-16 18:09:25,279] [INFO] DFAST_QC completed!
[2023-03-16 18:09:25,279] [INFO] Total running time: 0h1m53s