[2024-01-25 19:08:50,655] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:08:50,657] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:08:50,657] [INFO] DQC Reference Directory: /var/lib/cwl/stgdee42fe3-08d3-4f39-b742-9468295ce1d2/dqc_reference
[2024-01-25 19:08:51,868] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:08:51,869] [INFO] Task started: Prodigal
[2024-01-25 19:08:51,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg053dcf5d-1edf-4579-8d1e-70329fcea204/GCF_000428045.1_ASM42804v1_genomic.fna.gz | prodigal -d GCF_000428045.1_ASM42804v1_genomic.fna/cds.fna -a GCF_000428045.1_ASM42804v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:03,607] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:03,607] [INFO] Task started: HMMsearch
[2024-01-25 19:09:03,608] [INFO] Running command: hmmsearch --tblout GCF_000428045.1_ASM42804v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdee42fe3-08d3-4f39-b742-9468295ce1d2/dqc_reference/reference_markers.hmm GCF_000428045.1_ASM42804v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:03,916] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:03,918] [INFO] Found 6/6 markers.
[2024-01-25 19:09:03,955] [INFO] Query marker FASTA was written to GCF_000428045.1_ASM42804v1_genomic.fna/markers.fasta
[2024-01-25 19:09:03,956] [INFO] Task started: Blastn
[2024-01-25 19:09:03,956] [INFO] Running command: blastn -query GCF_000428045.1_ASM42804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdee42fe3-08d3-4f39-b742-9468295ce1d2/dqc_reference/reference_markers.fasta -out GCF_000428045.1_ASM42804v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:04,748] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:04,750] [INFO] Selected 25 target genomes.
[2024-01-25 19:09:04,751] [INFO] Target genome list was writen to GCF_000428045.1_ASM42804v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:04,766] [INFO] Task started: fastANI
[2024-01-25 19:09:04,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg053dcf5d-1edf-4579-8d1e-70329fcea204/GCF_000428045.1_ASM42804v1_genomic.fna.gz --refList GCF_000428045.1_ASM42804v1_genomic.fna/target_genomes.txt --output GCF_000428045.1_ASM42804v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:23,060] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:23,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdee42fe3-08d3-4f39-b742-9468295ce1d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:23,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdee42fe3-08d3-4f39-b742-9468295ce1d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:23,076] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:09:23,076] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:23,076] [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
Sedimenticola selenatireducens	strain=DSM 17993	GCA_000428045.1	191960	191960	type	True	99.9999	1504	1508	95	conclusive
Sedimenticola thiotaurini	strain=SIP-G1	GCA_001007875.1	1543721	1543721	type	True	81.2389	838	1508	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	79.3498	95	1508	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.3609	129	1508	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	77.3438	130	1508	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.1339	159	1508	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.1213	123	1508	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.7974	130	1508	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	76.5977	112	1508	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	76.4498	68	1508	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	76.4286	89	1508	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	76.3719	76	1508	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	76.2412	83	1508	95	below_threshold
Salinicola tamaricis	strain=F01	GCA_003006155.1	1771309	1771309	type	True	76.1912	67	1508	95	below_threshold
Thiocapsa marina	strain=5811	GCA_000223985.2	244573	244573	type	True	76.1759	88	1508	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	76.0579	94	1508	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	75.9642	84	1508	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	75.9455	50	1508	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	75.8334	53	1508	95	below_threshold
Stenotrophomonas rhizophila	strain=DSM14405	GCA_000661955.1	216778	216778	suspected-type	True	75.8187	55	1508	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	75.8119	78	1508	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	75.799	85	1508	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	75.7598	68	1508	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	75.5979	78	1508	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.5273	75	1508	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:23,078] [INFO] DFAST Taxonomy check result was written to GCF_000428045.1_ASM42804v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:23,078] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:23,078] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:23,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdee42fe3-08d3-4f39-b742-9468295ce1d2/dqc_reference/checkm_data
[2024-01-25 19:09:23,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:23,121] [INFO] Task started: CheckM
[2024-01-25 19:09:23,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000428045.1_ASM42804v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000428045.1_ASM42804v1_genomic.fna/checkm_input GCF_000428045.1_ASM42804v1_genomic.fna/checkm_result
[2024-01-25 19:09:59,498] [INFO] Task succeeded: CheckM
[2024-01-25 19:09:59,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:09:59,514] [INFO] ===== Completeness check finished =====
[2024-01-25 19:09:59,515] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:09:59,515] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000428045.1_ASM42804v1_genomic.fna/markers.fasta)
[2024-01-25 19:09:59,515] [INFO] Task started: Blastn
[2024-01-25 19:09:59,515] [INFO] Running command: blastn -query GCF_000428045.1_ASM42804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdee42fe3-08d3-4f39-b742-9468295ce1d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000428045.1_ASM42804v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:00,972] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:00,976] [INFO] Selected 16 target genomes.
[2024-01-25 19:10:00,976] [INFO] Target genome list was writen to GCF_000428045.1_ASM42804v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:01,027] [INFO] Task started: fastANI
[2024-01-25 19:10:01,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg053dcf5d-1edf-4579-8d1e-70329fcea204/GCF_000428045.1_ASM42804v1_genomic.fna.gz --refList GCF_000428045.1_ASM42804v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000428045.1_ASM42804v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:11,434] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:11,444] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:11,444] [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_000428045.1	s__Sedimenticola selenatireducens	99.9999	1504	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	98.15	98.15	0.90	0.90	2	conclusive
GCF_001007875.1	s__Sedimenticola thiotaurini	81.2417	837	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213265.1	s__Ideonella sp016213265	80.9104	62	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007713595.1	s__Sedimenticola thiotaurini_A	78.8312	444	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869585.1	s__BM503 sp002869585	78.5274	244	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__BM503	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007625115.1	s__Sedimenticola selenatireducens_A	78.4616	412	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011051715.1	s__HyVt-443 sp011051715	77.924	259	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003062205.1	s__Sedimenticola_A endophacoides	77.6505	247	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola_A	95.0	99.88	99.76	0.97	0.95	6	-
GCA_003972985.1	s__Thiolapillus sp003972985	77.3705	114	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiolapillus	95.0	99.52	99.52	0.88	0.88	2	-
GCA_003058495.1	s__Thiodiazotropha sp003058495	77.2657	156	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.61	99.54	0.96	0.95	6	-
GCA_011051655.1	s__DRKS01 sp011051655	76.9899	154	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490795.1	s__DRKS01 sp015490795	76.87	98	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	99.53	99.46	0.94	0.93	5	-
GCA_003696465.1	s__J044 sp003696465	76.3947	67	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J044;f__J044;g__J044	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966155.1	s__Halomonas nitroreducens	75.9331	86	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:11,445] [INFO] GTDB search result was written to GCF_000428045.1_ASM42804v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:11,447] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:11,451] [INFO] DFAST_QC result json was written to GCF_000428045.1_ASM42804v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:11,451] [INFO] DFAST_QC completed!
[2024-01-25 19:10:11,451] [INFO] Total running time: 0h1m21s