[2024-01-24 15:18:18,621] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:18,623] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:18,623] [INFO] DQC Reference Directory: /var/lib/cwl/stgba399094-008e-40cb-9b17-7b98076578a1/dqc_reference
[2024-01-24 15:18:19,870] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:19,871] [INFO] Task started: Prodigal
[2024-01-24 15:18:19,871] [INFO] Running command: gunzip -c /var/lib/cwl/stge3346ef7-90e2-4f01-b3d9-6a77d63d2474/GCF_004137685.1_ASM413768v1_genomic.fna.gz | prodigal -d GCF_004137685.1_ASM413768v1_genomic.fna/cds.fna -a GCF_004137685.1_ASM413768v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:35,850] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:35,851] [INFO] Task started: HMMsearch
[2024-01-24 15:18:35,851] [INFO] Running command: hmmsearch --tblout GCF_004137685.1_ASM413768v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba399094-008e-40cb-9b17-7b98076578a1/dqc_reference/reference_markers.hmm GCF_004137685.1_ASM413768v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:36,203] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:36,204] [INFO] Found 6/6 markers.
[2024-01-24 15:18:36,261] [INFO] Query marker FASTA was written to GCF_004137685.1_ASM413768v1_genomic.fna/markers.fasta
[2024-01-24 15:18:36,261] [INFO] Task started: Blastn
[2024-01-24 15:18:36,261] [INFO] Running command: blastn -query GCF_004137685.1_ASM413768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba399094-008e-40cb-9b17-7b98076578a1/dqc_reference/reference_markers.fasta -out GCF_004137685.1_ASM413768v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:37,308] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:37,311] [INFO] Selected 25 target genomes.
[2024-01-24 15:18:37,311] [INFO] Target genome list was writen to GCF_004137685.1_ASM413768v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:37,322] [INFO] Task started: fastANI
[2024-01-24 15:18:37,323] [INFO] Running command: fastANI --query /var/lib/cwl/stge3346ef7-90e2-4f01-b3d9-6a77d63d2474/GCF_004137685.1_ASM413768v1_genomic.fna.gz --refList GCF_004137685.1_ASM413768v1_genomic.fna/target_genomes.txt --output GCF_004137685.1_ASM413768v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:05,375] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:05,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba399094-008e-40cb-9b17-7b98076578a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:05,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba399094-008e-40cb-9b17-7b98076578a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:05,481] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:05,482] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:05,482] [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
Lichenibacterium minor	strain=RmlP026	GCA_004137685.1	2316528	2316528	type	True	100.0	1873	1879	95	conclusive
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	84.5586	1175	1879	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	77.506	639	1879	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.4739	665	1879	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.4662	389	1879	95	below_threshold
Alsobacter metallidurans	strain=CGMCC 1.12214	GCA_014636935.1	340221	340221	type	True	77.4461	483	1879	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	77.4055	537	1879	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	77.3738	609	1879	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	77.3284	335	1879	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	77.3153	388	1879	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.3112	488	1879	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	77.2983	716	1879	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	77.2977	486	1879	95	below_threshold
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	77.2485	543	1879	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	77.2443	572	1879	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.225	424	1879	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	77.2023	531	1879	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	77.2013	433	1879	95	below_threshold
Methylobacterium soli	strain=YIM 48816	GCA_008806385.1	553447	553447	type	True	77.1874	479	1879	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	77.1797	388	1879	95	below_threshold
Roseiarcus fermentans	strain=DSM 24875	GCA_003315135.1	1473586	1473586	type	True	77.1474	515	1879	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	77.0546	240	1879	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_002937135.1	1074	1074	suspected-type	True	76.916	346	1879	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_003258765.1	1074	1074	suspected-type	True	76.8708	343	1879	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	74.823	333	1879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:05,556] [INFO] DFAST Taxonomy check result was written to GCF_004137685.1_ASM413768v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:05,557] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:05,557] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:05,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba399094-008e-40cb-9b17-7b98076578a1/dqc_reference/checkm_data
[2024-01-24 15:19:05,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:05,700] [INFO] Task started: CheckM
[2024-01-24 15:19:05,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004137685.1_ASM413768v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004137685.1_ASM413768v1_genomic.fna/checkm_input GCF_004137685.1_ASM413768v1_genomic.fna/checkm_result
[2024-01-24 15:20:03,701] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:03,702] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:03,730] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:03,730] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:03,730] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004137685.1_ASM413768v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:03,731] [INFO] Task started: Blastn
[2024-01-24 15:20:03,731] [INFO] Running command: blastn -query GCF_004137685.1_ASM413768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba399094-008e-40cb-9b17-7b98076578a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_004137685.1_ASM413768v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:05,587] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:05,593] [INFO] Selected 25 target genomes.
[2024-01-24 15:20:05,593] [INFO] Target genome list was writen to GCF_004137685.1_ASM413768v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:05,616] [INFO] Task started: fastANI
[2024-01-24 15:20:05,616] [INFO] Running command: fastANI --query /var/lib/cwl/stge3346ef7-90e2-4f01-b3d9-6a77d63d2474/GCF_004137685.1_ASM413768v1_genomic.fna.gz --refList GCF_004137685.1_ASM413768v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004137685.1_ASM413768v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:31,316] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:31,344] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:31,345] [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_004137685.1	s__Lichenihabitans minor	100.0	1873	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004137085.1	s__Lichenihabitans ramalinae	84.5923	1170	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Lichenihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901457705.2	s__RH-AL1 sp901457705	77.8538	496	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__RH-AL1	95.0	99.94	99.94	0.99	0.99	3	-
GCF_004745635.1	s__Methylobacterium sp004745635	77.6475	661	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765775.1	s__RH-AL1 sp009765775	77.4969	354	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__RH-AL1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716745.1	s__GCA-013693735 sp016716745	77.4549	490	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004004555.2	s__Methylobacterium sp004004555	77.4457	671	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046185.1	s__Phreatobacter oligotrophus	77.4454	392	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262405.1	s__Microvirga lotononidis	77.3462	333	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112625.1	s__Methylobacterium sp900112625	77.3081	592	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_014196925.1	s__Chelatococcus_A caeni	77.288	491	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_902141855.1	s__Methylobacterium dankookense	77.2423	544	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168195.1	s__Bosea thiooxidans	77.2375	428	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.77	99.77	0.94	0.94	2	-
GCF_003008515.1	s__Phreatobacter cathodiphilus	77.2049	427	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793505.1	s__GCA-013693735 sp016793505	77.198	454	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188155.2	s__Methylocystis sp000188155	77.1959	258	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745395.1	s__Methylocystis sp016745395	77.1846	239	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315135.1	s__Roseiarcus fermentans	77.1816	509	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Roseiarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806385.1	s__Methylobacterium soli	77.1667	483	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295925.1	s__Bosea sp001295925	77.0232	321	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000283235.1	s__Methylocystis parvus	76.9916	246	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002298965.1	s__Pinisolibacter sp002298965	76.9058	352	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164915.1	s__Roseiarcus sp003164915	76.7331	357	1879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Roseiarcus	95.0	99.60	99.60	0.89	0.89	2	-
GCF_900091475.1	s__Micromonospora chersina	74.8215	334	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.87	95.82	0.87	0.87	3	-
GCA_013822085.1	s__WM-009 sp013822085	74.7449	97	1879	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__WM-009	95.0	99.63	99.61	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:31,346] [INFO] GTDB search result was written to GCF_004137685.1_ASM413768v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:31,347] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:31,352] [INFO] DFAST_QC result json was written to GCF_004137685.1_ASM413768v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:31,352] [INFO] DFAST_QC completed!
[2024-01-24 15:20:31,353] [INFO] Total running time: 0h2m13s