[2023-07-01 04:52:02,887] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:52:02,890] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:52:02,891] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe228661-0389-4ab9-8aad-722a905914f6/dqc_reference
[2023-07-01 04:52:04,075] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:52:04,076] [INFO] Task started: Prodigal
[2023-07-01 04:52:04,076] [INFO] Running command: gunzip -c /var/lib/cwl/stga1159abd-2e92-4e04-a218-27a66b1807d9/GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna.gz | prodigal -d GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/cds.fna -a GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:52:16,444] [INFO] Task succeeded: Prodigal
[2023-07-01 04:52:16,444] [INFO] Task started: HMMsearch
[2023-07-01 04:52:16,444] [INFO] Running command: hmmsearch --tblout GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe228661-0389-4ab9-8aad-722a905914f6/dqc_reference/reference_markers.hmm GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:52:16,660] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:52:16,661] [INFO] Found 6/6 markers.
[2023-07-01 04:52:16,690] [INFO] Query marker FASTA was written to GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/markers.fasta
[2023-07-01 04:52:16,690] [INFO] Task started: Blastn
[2023-07-01 04:52:16,690] [INFO] Running command: blastn -query GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe228661-0389-4ab9-8aad-722a905914f6/dqc_reference/reference_markers.fasta -out GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:52:17,407] [INFO] Task succeeded: Blastn
[2023-07-01 04:52:17,411] [INFO] Selected 24 target genomes.
[2023-07-01 04:52:17,411] [INFO] Target genome list was writen to GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/target_genomes.txt
[2023-07-01 04:52:17,412] [INFO] Task started: fastANI
[2023-07-01 04:52:17,412] [INFO] Running command: fastANI --query /var/lib/cwl/stga1159abd-2e92-4e04-a218-27a66b1807d9/GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna.gz --refList GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/target_genomes.txt --output GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:52:33,488] [INFO] Task succeeded: fastANI
[2023-07-01 04:52:33,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe228661-0389-4ab9-8aad-722a905914f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:52:33,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe228661-0389-4ab9-8aad-722a905914f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:52:33,504] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 04:52:33,504] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 04:52:33,505] [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
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	78.24	290	1053	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	77.8307	227	1053	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.8065	274	1053	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	77.8055	327	1053	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	77.3668	187	1053	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	77.1925	196	1053	95	below_threshold
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001640105.1	1763535	1763535	type	True	77.0781	162	1053	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	77.0767	171	1053	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	77.0509	158	1053	95	below_threshold
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001761385.1	1763535	1763535	type	True	77.0457	160	1053	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	77.0275	144	1053	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	77.0219	194	1053	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	76.896	140	1053	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	76.8701	165	1053	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	76.769	158	1053	95	below_threshold
Simplicispira psychrophila	strain=DSM 11588	GCA_000688255.1	80882	80882	type	True	76.768	157	1053	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	76.7668	177	1053	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	76.7235	181	1053	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	76.7117	188	1053	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	76.379	141	1053	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	76.0832	89	1053	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 04:52:33,539] [INFO] DFAST Taxonomy check result was written to GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/tc_result.tsv
[2023-07-01 04:52:33,539] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:52:33,540] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:52:33,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe228661-0389-4ab9-8aad-722a905914f6/dqc_reference/checkm_data
[2023-07-01 04:52:33,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:52:33,572] [INFO] Task started: CheckM
[2023-07-01 04:52:33,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/checkm_input GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/checkm_result
[2023-07-01 04:53:13,121] [INFO] Task succeeded: CheckM
[2023-07-01 04:53:13,122] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.56%
Contamintation: 1.85%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-07-01 04:53:13,139] [INFO] ===== Completeness check finished =====
[2023-07-01 04:53:13,139] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:53:13,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/markers.fasta)
[2023-07-01 04:53:13,140] [INFO] Task started: Blastn
[2023-07-01 04:53:13,140] [INFO] Running command: blastn -query GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe228661-0389-4ab9-8aad-722a905914f6/dqc_reference/reference_markers_gtdb.fasta -out GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:53:14,427] [INFO] Task succeeded: Blastn
[2023-07-01 04:53:14,430] [INFO] Selected 16 target genomes.
[2023-07-01 04:53:14,430] [INFO] Target genome list was writen to GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:53:14,431] [INFO] Task started: fastANI
[2023-07-01 04:53:14,431] [INFO] Running command: fastANI --query /var/lib/cwl/stga1159abd-2e92-4e04-a218-27a66b1807d9/GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna.gz --refList GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/target_genomes_gtdb.txt --output GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:53:24,283] [INFO] Task succeeded: fastANI
[2023-07-01 04:53:24,296] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 04:53:24,296] [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_903870145.1	s__Limnohabitans_A sp903870145	99.7844	874	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.83	99.72	0.91	0.84	26	conclusive
GCF_001412575.1	s__Limnohabitans_A sp001412575	79.4547	431	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.90	97.72	0.94	0.91	3	-
GCF_003063375.1	s__Limnohabitans_A sp003063375	79.0423	378	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001269365.1	s__Limnohabitans_A sp001269365	79.0087	409	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903856875.1	s__Limnohabitans_A sp903856875	78.7462	254	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009928125.1	s__Limnohabitans_A sp009928125	78.5576	277	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	98.84	98.65	0.83	0.81	5	-
GCA_005789685.1	s__Limnohabitans_A sp005789685	78.4813	223	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903961095.1	s__Limnohabitans_A sp903961095	78.2051	317	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.26	99.25	0.86	0.84	3	-
GCA_017848645.1	s__Limnohabitans_A sp017848645	78.0832	298	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.74	96.96	0.88	0.84	5	-
GCF_000293865.2	s__Limnohabitans_A sp000293865	78.0061	295	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255935.1	s__Limnohabitans_A sp002255935	77.9044	308	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822825.1	s__Limnohabitans_A sp903822825	77.8605	262	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.95	99.93	0.93	0.91	3	-
GCF_003063355.1	s__Limnohabitans_A sp003063355	77.8586	311	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903840825.1	s__Rhodoferax sp903840825	76.8916	129	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103645.1	s__Oryzisolibacter propanilivorax	76.5706	127	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oryzisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780365.1	s__Acidovorax sp018780365	76.4923	127	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 04:53:24,298] [INFO] GTDB search result was written to GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/result_gtdb.tsv
[2023-07-01 04:53:24,298] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:53:24,302] [INFO] DFAST_QC result json was written to GCA_903941035.1_freshwater_MAG_---_Loc090721-8m_bin-539_genomic.fna/dqc_result.json
[2023-07-01 04:53:24,302] [INFO] DFAST_QC completed!
[2023-07-01 04:53:24,302] [INFO] Total running time: 0h1m21s