[2024-01-24 13:58:11,012] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:11,014] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:11,015] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdc7ef5d-c478-43d1-b099-82005866ea4a/dqc_reference
[2024-01-24 13:58:12,441] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,442] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,443] [INFO] Running command: gunzip -c /var/lib/cwl/stgee7758cd-88e7-4a19-ab55-a5e9f9b32d00/GCF_020103775.1_ASM2010377v1_genomic.fna.gz | prodigal -d GCF_020103775.1_ASM2010377v1_genomic.fna/cds.fna -a GCF_020103775.1_ASM2010377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:48,298] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:48,299] [INFO] Task started: HMMsearch
[2024-01-24 13:58:48,299] [INFO] Running command: hmmsearch --tblout GCF_020103775.1_ASM2010377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdc7ef5d-c478-43d1-b099-82005866ea4a/dqc_reference/reference_markers.hmm GCF_020103775.1_ASM2010377v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:48,695] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:48,696] [INFO] Found 6/6 markers.
[2024-01-24 13:58:48,772] [INFO] Query marker FASTA was written to GCF_020103775.1_ASM2010377v1_genomic.fna/markers.fasta
[2024-01-24 13:58:48,772] [INFO] Task started: Blastn
[2024-01-24 13:58:48,772] [INFO] Running command: blastn -query GCF_020103775.1_ASM2010377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdc7ef5d-c478-43d1-b099-82005866ea4a/dqc_reference/reference_markers.fasta -out GCF_020103775.1_ASM2010377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:49,568] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:49,571] [INFO] Selected 22 target genomes.
[2024-01-24 13:58:49,572] [INFO] Target genome list was writen to GCF_020103775.1_ASM2010377v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:49,593] [INFO] Task started: fastANI
[2024-01-24 13:58:49,593] [INFO] Running command: fastANI --query /var/lib/cwl/stgee7758cd-88e7-4a19-ab55-a5e9f9b32d00/GCF_020103775.1_ASM2010377v1_genomic.fna.gz --refList GCF_020103775.1_ASM2010377v1_genomic.fna/target_genomes.txt --output GCF_020103775.1_ASM2010377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:33,361] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:33,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdc7ef5d-c478-43d1-b099-82005866ea4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:33,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdc7ef5d-c478-43d1-b099-82005866ea4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:33,378] [INFO] Found 22 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:59:33,378] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:59:33,378] [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
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	100.0	3012	3016	95	inconclusive
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	97.3406	2807	3016	95	inconclusive
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	95.1585	2743	3016	95	inconclusive
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	81.0204	1565	3016	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	80.9679	1583	3016	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	80.9132	1524	3016	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	80.8267	1218	3016	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	80.8219	1371	3016	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	80.792	1450	3016	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	80.7754	1319	3016	95	below_threshold
Myxococcus virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	80.7182	1308	3016	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	80.6926	1584	3016	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	80.6871	1568	3016	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	80.6268	1421	3016	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	80.6184	1411	3016	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	80.6152	1512	3016	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_900101365.1	381306	381306	type	True	75.2988	145	3016	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_001399755.1	381306	381306	type	True	75.2585	142	3016	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	75.2282	148	3016	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.9067	192	3016	95	below_threshold
Nocardia terpenica	strain=IFM 0706	GCA_013186535.1	455432	455432	type	True	74.8707	247	3016	95	below_threshold
Kribbella sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	74.7531	172	3016	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:33,380] [INFO] DFAST Taxonomy check result was written to GCF_020103775.1_ASM2010377v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:33,380] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:33,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:33,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdc7ef5d-c478-43d1-b099-82005866ea4a/dqc_reference/checkm_data
[2024-01-24 13:59:33,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:33,465] [INFO] Task started: CheckM
[2024-01-24 13:59:33,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020103775.1_ASM2010377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020103775.1_ASM2010377v1_genomic.fna/checkm_input GCF_020103775.1_ASM2010377v1_genomic.fna/checkm_result
[2024-01-24 14:01:54,194] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:54,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:01:54,217] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:54,217] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:54,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020103775.1_ASM2010377v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:54,217] [INFO] Task started: Blastn
[2024-01-24 14:01:54,217] [INFO] Running command: blastn -query GCF_020103775.1_ASM2010377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdc7ef5d-c478-43d1-b099-82005866ea4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_020103775.1_ASM2010377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:55,518] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:55,522] [INFO] Selected 8 target genomes.
[2024-01-24 14:01:55,522] [INFO] Target genome list was writen to GCF_020103775.1_ASM2010377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:55,529] [INFO] Task started: fastANI
[2024-01-24 14:01:55,529] [INFO] Running command: fastANI --query /var/lib/cwl/stgee7758cd-88e7-4a19-ab55-a5e9f9b32d00/GCF_020103775.1_ASM2010377v1_genomic.fna.gz --refList GCF_020103775.1_ASM2010377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020103775.1_ASM2010377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:02:16,777] [INFO] Task succeeded: fastANI
[2024-01-24 14:02:16,784] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:02:16,784] [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_900109545.1	s__Stigmatella aurantiaca	97.3461	2806	3016	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.281	N/A	N/A	N/A	N/A	1	conclusive
GCF_900111745.1	s__Stigmatella erecta	95.1528	2744	3016	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.281	N/A	N/A	N/A	N/A	1	-
GCF_000165485.1	s__Stigmatella aurantiaca_A	88.0334	2454	3016	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016926755.1	s__Hyalangium sp016926755	83.16	1559	3016	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Hyalangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737315.1	s__Hyalangium minutum	82.4854	1777	3016	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Hyalangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933655.1	s__Myxococcus fallax	80.9327	1521	3016	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016887565.1	s__Archangium violaceum_B	80.8412	1687	3016	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027285.1	s__Archangium gephyra	80.6877	1587	3016	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:02:16,786] [INFO] GTDB search result was written to GCF_020103775.1_ASM2010377v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:02:16,787] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:02:16,790] [INFO] DFAST_QC result json was written to GCF_020103775.1_ASM2010377v1_genomic.fna/dqc_result.json
[2024-01-24 14:02:16,790] [INFO] DFAST_QC completed!
[2024-01-24 14:02:16,791] [INFO] Total running time: 0h4m6s