[2023-06-28 01:42:51,416] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:42:51,419] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:42:51,420] [INFO] DQC Reference Directory: /var/lib/cwl/stged18319d-b8d7-4278-bb80-3637c9ddf2f4/dqc_reference
[2023-06-28 01:42:52,674] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:42:52,675] [INFO] Task started: Prodigal
[2023-06-28 01:42:52,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c06d60f-2a4d-4ba2-8e67-c49f962f4c76/GCA_026041365.1_ASM2604136v1_genomic.fna.gz | prodigal -d GCA_026041365.1_ASM2604136v1_genomic.fna/cds.fna -a GCA_026041365.1_ASM2604136v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:43:05,694] [INFO] Task succeeded: Prodigal
[2023-06-28 01:43:05,694] [INFO] Task started: HMMsearch
[2023-06-28 01:43:05,694] [INFO] Running command: hmmsearch --tblout GCA_026041365.1_ASM2604136v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged18319d-b8d7-4278-bb80-3637c9ddf2f4/dqc_reference/reference_markers.hmm GCA_026041365.1_ASM2604136v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:43:05,946] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:43:05,948] [INFO] Found 6/6 markers.
[2023-06-28 01:43:05,989] [INFO] Query marker FASTA was written to GCA_026041365.1_ASM2604136v1_genomic.fna/markers.fasta
[2023-06-28 01:43:05,990] [INFO] Task started: Blastn
[2023-06-28 01:43:05,990] [INFO] Running command: blastn -query GCA_026041365.1_ASM2604136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged18319d-b8d7-4278-bb80-3637c9ddf2f4/dqc_reference/reference_markers.fasta -out GCA_026041365.1_ASM2604136v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:43:06,724] [INFO] Task succeeded: Blastn
[2023-06-28 01:43:06,728] [INFO] Selected 31 target genomes.
[2023-06-28 01:43:06,729] [INFO] Target genome list was writen to GCA_026041365.1_ASM2604136v1_genomic.fna/target_genomes.txt
[2023-06-28 01:43:06,730] [INFO] Task started: fastANI
[2023-06-28 01:43:06,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c06d60f-2a4d-4ba2-8e67-c49f962f4c76/GCA_026041365.1_ASM2604136v1_genomic.fna.gz --refList GCA_026041365.1_ASM2604136v1_genomic.fna/target_genomes.txt --output GCA_026041365.1_ASM2604136v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:43:26,304] [INFO] Task succeeded: fastANI
[2023-06-28 01:43:26,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged18319d-b8d7-4278-bb80-3637c9ddf2f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:43:26,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged18319d-b8d7-4278-bb80-3637c9ddf2f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:43:26,317] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:43:26,317] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 01:43:26,317] [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	77.0959	122	1602	95	below_threshold
Sedimenticola thiotaurini	strain=SIP-G1	GCA_001007875.1	1543721	1543721	type	True	76.8156	122	1602	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	76.772	58	1602	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	76.7455	62	1602	95	below_threshold
Sulfuriflexus mobilis	strain=aks1	GCA_003967195.1	1811807	1811807	type	True	76.7394	57	1602	95	below_threshold
Thiohalophilus thiocyanatoxydans	strain=DSM 16326	GCA_004366735.1	381308	381308	type	True	76.6156	61	1602	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.452	77	1602	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.3571	82	1602	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.2809	56	1602	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.2182	76	1602	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.1963	74	1602	95	below_threshold
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	76.0979	51	1602	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.0919	74	1602	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	76.0556	76	1602	95	below_threshold
Halochromatium roseum	strain=DSM 18859	GCA_016653315.1	391920	391920	type	True	75.9317	65	1602	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:43:26,319] [INFO] DFAST Taxonomy check result was written to GCA_026041365.1_ASM2604136v1_genomic.fna/tc_result.tsv
[2023-06-28 01:43:26,319] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:43:26,319] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:43:26,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged18319d-b8d7-4278-bb80-3637c9ddf2f4/dqc_reference/checkm_data
[2023-06-28 01:43:26,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:43:26,367] [INFO] Task started: CheckM
[2023-06-28 01:43:26,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026041365.1_ASM2604136v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026041365.1_ASM2604136v1_genomic.fna/checkm_input GCA_026041365.1_ASM2604136v1_genomic.fna/checkm_result
[2023-06-28 01:44:08,191] [INFO] Task succeeded: CheckM
[2023-06-28 01:44:08,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 01:44:08,208] [INFO] ===== Completeness check finished =====
[2023-06-28 01:44:08,208] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:44:08,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026041365.1_ASM2604136v1_genomic.fna/markers.fasta)
[2023-06-28 01:44:08,208] [INFO] Task started: Blastn
[2023-06-28 01:44:08,208] [INFO] Running command: blastn -query GCA_026041365.1_ASM2604136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged18319d-b8d7-4278-bb80-3637c9ddf2f4/dqc_reference/reference_markers_gtdb.fasta -out GCA_026041365.1_ASM2604136v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:44:09,316] [INFO] Task succeeded: Blastn
[2023-06-28 01:44:09,319] [INFO] Selected 6 target genomes.
[2023-06-28 01:44:09,319] [INFO] Target genome list was writen to GCA_026041365.1_ASM2604136v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:44:09,320] [INFO] Task started: fastANI
[2023-06-28 01:44:09,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c06d60f-2a4d-4ba2-8e67-c49f962f4c76/GCA_026041365.1_ASM2604136v1_genomic.fna.gz --refList GCA_026041365.1_ASM2604136v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026041365.1_ASM2604136v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:44:15,940] [INFO] Task succeeded: fastANI
[2023-06-28 01:44:15,947] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 01:44:15,947] [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_001709035.1	s__Thiodiazotropha endoloripes_B	99.6025	1523	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.26	97.31	0.93	0.86	11	conclusive
GCF_001708965.1	s__Thiodiazotropha endoloripes	92.0915	1352	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.62	99.43	0.97	0.94	9	-
GCA_016842065.1	s__Thiodiazotropha sp016842065	89.4246	1279	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019100305.1	s__Thiodiazotropha sp019100305	89.2509	981	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003676145.1	s__Thiodiazotropha endolucinida	89.2327	1293	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	97.91	96.39	0.93	0.89	26	-
GCA_003058495.1	s__Thiodiazotropha sp003058495	78.2416	408	1602	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.61	99.54	0.96	0.95	6	-
--------------------------------------------------------------------------------
[2023-06-28 01:44:15,948] [INFO] GTDB search result was written to GCA_026041365.1_ASM2604136v1_genomic.fna/result_gtdb.tsv
[2023-06-28 01:44:15,949] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:44:15,952] [INFO] DFAST_QC result json was written to GCA_026041365.1_ASM2604136v1_genomic.fna/dqc_result.json
[2023-06-28 01:44:15,952] [INFO] DFAST_QC completed!
[2023-06-28 01:44:15,952] [INFO] Total running time: 0h1m25s