[2023-03-16 23:05:03,923] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,924] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg5630cc91-ecd4-4abf-9eb6-f2609d358880/dqc_reference
[2023-03-16 23:05:05,251] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,251] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,251] [INFO] Running command: cat /var/lib/cwl/stg361d422b-8f90-4027-b20b-66623ea93b4e/OceanDNA-b30176.fa | prodigal -d OceanDNA-b30176/cds.fna -a OceanDNA-b30176/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:23,424] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:23,424] [INFO] Task started: HMMsearch
[2023-03-16 23:05:23,424] [INFO] Running command: hmmsearch --tblout OceanDNA-b30176/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5630cc91-ecd4-4abf-9eb6-f2609d358880/dqc_reference/reference_markers.hmm OceanDNA-b30176/protein.faa > /dev/null
[2023-03-16 23:05:23,661] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:23,662] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg361d422b-8f90-4027-b20b-66623ea93b4e/OceanDNA-b30176.fa]
[2023-03-16 23:05:23,684] [INFO] Query marker FASTA was written to OceanDNA-b30176/markers.fasta
[2023-03-16 23:05:23,684] [INFO] Task started: Blastn
[2023-03-16 23:05:23,684] [INFO] Running command: blastn -query OceanDNA-b30176/markers.fasta -db /var/lib/cwl/stg5630cc91-ecd4-4abf-9eb6-f2609d358880/dqc_reference/reference_markers.fasta -out OceanDNA-b30176/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:24,310] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:24,311] [INFO] Selected 25 target genomes.
[2023-03-16 23:05:24,311] [INFO] Target genome list was writen to OceanDNA-b30176/target_genomes.txt
[2023-03-16 23:05:24,325] [INFO] Task started: fastANI
[2023-03-16 23:05:24,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg361d422b-8f90-4027-b20b-66623ea93b4e/OceanDNA-b30176.fa --refList OceanDNA-b30176/target_genomes.txt --output OceanDNA-b30176/fastani_result.tsv --threads 1
[2023-03-16 23:05:40,983] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:40,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5630cc91-ecd4-4abf-9eb6-f2609d358880/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:40,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5630cc91-ecd4-4abf-9eb6-f2609d358880/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:40,997] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:40,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:05:40,997] [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
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	78.4004	358	953	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	78.1879	397	953	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	78.161	395	953	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.8348	260	953	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	77.8346	252	953	95	below_threshold
Sulfitobacter guttiformis	strain=DSM 11458	GCA_003610455.1	74349	74349	type	True	77.8313	332	953	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	77.2742	209	953	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.2221	203	953	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.2178	246	953	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.0755	211	953	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.0231	230	953	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	76.3806	133	953	95	below_threshold
Tritonibacter scottomollicae	strain=DSM 25328	GCA_003003215.1	483013	483013	type	True	76.3276	128	953	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	76.3048	119	953	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	76.2895	120	953	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	76.2331	81	953	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	76.1959	105	953	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	75.9908	54	953	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.9905	102	953	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	75.9767	93	953	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	75.9297	93	953	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	75.748	79	953	95	below_threshold
Jannaschia aquimarina	strain=DSM 28248	GCA_900188045.1	935700	935700	type	True	75.5032	59	953	95	below_threshold
Jannaschia aquimarina	strain=GSW-M26	GCA_000877395.1	935700	935700	type	True	75.4917	60	953	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:05:40,998] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30176/tc_result.tsv
[2023-03-16 23:05:40,998] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:40,998] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:40,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5630cc91-ecd4-4abf-9eb6-f2609d358880/dqc_reference/checkm_data
[2023-03-16 23:05:40,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:41,003] [INFO] Task started: CheckM
[2023-03-16 23:05:41,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30176/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30176/checkm_input OceanDNA-b30176/checkm_result
[2023-03-16 23:06:28,063] [INFO] Task succeeded: CheckM
[2023-03-16 23:06:28,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:06:28,066] [INFO] ===== Completeness check finished =====
[2023-03-16 23:06:28,066] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:06:28,066] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30176/markers.fasta)
[2023-03-16 23:06:28,066] [INFO] Task started: Blastn
[2023-03-16 23:06:28,066] [INFO] Running command: blastn -query OceanDNA-b30176/markers.fasta -db /var/lib/cwl/stg5630cc91-ecd4-4abf-9eb6-f2609d358880/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30176/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:06:29,065] [INFO] Task succeeded: Blastn
[2023-03-16 23:06:29,066] [INFO] Selected 25 target genomes.
[2023-03-16 23:06:29,066] [INFO] Target genome list was writen to OceanDNA-b30176/target_genomes_gtdb.txt
[2023-03-16 23:06:29,648] [INFO] Task started: fastANI
[2023-03-16 23:06:29,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg361d422b-8f90-4027-b20b-66623ea93b4e/OceanDNA-b30176.fa --refList OceanDNA-b30176/target_genomes_gtdb.txt --output OceanDNA-b30176/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:06:46,725] [INFO] Task succeeded: fastANI
[2023-03-16 23:06:46,740] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:06:46,740] [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_014196805.1	s__Sulfitobacter undariae	78.4004	358	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622405.1	s__Sulfitobacter donghicola	78.1604	395	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000622325.1	s__Sulfitobacter geojensis	77.8346	252	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_003610455.1	s__Sulfitobacter guttiformis	77.8313	332	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013282155.1	s__Sulfitobacter sp013282155	77.6745	273	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_000156335.1	s__Sulfitobacter sp000156335	77.4677	260	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	77.3012	226	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018200035.1	s__Sulfitobacter sp018200035	77.2949	326	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103185.1	s__Sulfitobacter litoralis	77.2742	209	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCA_017854675.1	s__Sulfitobacter sp017854675	77.2551	190	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	77.2178	246	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.1658	238	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	77.1506	216	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.06	229	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_900112755.1	s__Sulfitobacter brevis	76.9737	202	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	76.8145	215	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	76.408	89	953	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_003003215.1	s__Epibacterium scottomollicae	76.3276	128	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184895.1	s__Flavimaricola marinus	76.2331	81	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001292625.1	s__Shimia sp001292625	76.22	116	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014899185.1	s__Pseudooceanicola antarcticus_A	76.1808	106	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874255.1	s__Epibacterium sp001874255	76.0999	103	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169455.1	s__Pseudophaeobacter sp000169455	75.9043	94	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314705.1	s__Aquicoccus sp001314705	75.6412	92	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689705.1	s__HKCCE3408 sp015689705	75.6291	50	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:06:46,740] [INFO] GTDB search result was written to OceanDNA-b30176/result_gtdb.tsv
[2023-03-16 23:06:46,740] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:06:46,743] [INFO] DFAST_QC result json was written to OceanDNA-b30176/dqc_result.json
[2023-03-16 23:06:46,743] [INFO] DFAST_QC completed!
[2023-03-16 23:06:46,743] [INFO] Total running time: 0h1m43s