[2023-06-29 12:29:19,287] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:29:19,289] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:29:19,289] [INFO] DQC Reference Directory: /var/lib/cwl/stg76fc150f-6e33-4f95-975d-47dae4daaee7/dqc_reference
[2023-06-29 12:29:20,450] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:29:20,451] [INFO] Task started: Prodigal
[2023-06-29 12:29:20,451] [INFO] Running command: gunzip -c /var/lib/cwl/stg59da1139-e197-4f7a-839c-ae595bebb9a5/GCA_021648685.1_ASM2164868v1_genomic.fna.gz | prodigal -d GCA_021648685.1_ASM2164868v1_genomic.fna/cds.fna -a GCA_021648685.1_ASM2164868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:29:28,406] [INFO] Task succeeded: Prodigal
[2023-06-29 12:29:28,407] [INFO] Task started: HMMsearch
[2023-06-29 12:29:28,407] [INFO] Running command: hmmsearch --tblout GCA_021648685.1_ASM2164868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76fc150f-6e33-4f95-975d-47dae4daaee7/dqc_reference/reference_markers.hmm GCA_021648685.1_ASM2164868v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:29:28,666] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:29:28,668] [INFO] Found 6/6 markers.
[2023-06-29 12:29:28,699] [INFO] Query marker FASTA was written to GCA_021648685.1_ASM2164868v1_genomic.fna/markers.fasta
[2023-06-29 12:29:28,699] [INFO] Task started: Blastn
[2023-06-29 12:29:28,700] [INFO] Running command: blastn -query GCA_021648685.1_ASM2164868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76fc150f-6e33-4f95-975d-47dae4daaee7/dqc_reference/reference_markers.fasta -out GCA_021648685.1_ASM2164868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:29:29,444] [INFO] Task succeeded: Blastn
[2023-06-29 12:29:29,448] [INFO] Selected 35 target genomes.
[2023-06-29 12:29:29,449] [INFO] Target genome list was writen to GCA_021648685.1_ASM2164868v1_genomic.fna/target_genomes.txt
[2023-06-29 12:29:29,453] [INFO] Task started: fastANI
[2023-06-29 12:29:29,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg59da1139-e197-4f7a-839c-ae595bebb9a5/GCA_021648685.1_ASM2164868v1_genomic.fna.gz --refList GCA_021648685.1_ASM2164868v1_genomic.fna/target_genomes.txt --output GCA_021648685.1_ASM2164868v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:29:49,556] [INFO] Task succeeded: fastANI
[2023-06-29 12:29:49,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76fc150f-6e33-4f95-975d-47dae4daaee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:29:49,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76fc150f-6e33-4f95-975d-47dae4daaee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:29:49,563] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:29:49,563] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:29:49,563] [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
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.9398	50	935	95	below_threshold
Sedimenticola selenatireducens	strain=DSM 17993	GCA_000428045.1	191960	191960	type	True	76.4204	90	935	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.1009	57	935	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.0175	60	935	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:29:49,565] [INFO] DFAST Taxonomy check result was written to GCA_021648685.1_ASM2164868v1_genomic.fna/tc_result.tsv
[2023-06-29 12:29:49,566] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:29:49,566] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:29:49,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76fc150f-6e33-4f95-975d-47dae4daaee7/dqc_reference/checkm_data
[2023-06-29 12:29:49,568] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:29:49,599] [INFO] Task started: CheckM
[2023-06-29 12:29:49,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021648685.1_ASM2164868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021648685.1_ASM2164868v1_genomic.fna/checkm_input GCA_021648685.1_ASM2164868v1_genomic.fna/checkm_result
[2023-06-29 12:30:18,578] [INFO] Task succeeded: CheckM
[2023-06-29 12:30:18,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:30:18,602] [INFO] ===== Completeness check finished =====
[2023-06-29 12:30:18,602] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:30:18,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021648685.1_ASM2164868v1_genomic.fna/markers.fasta)
[2023-06-29 12:30:18,603] [INFO] Task started: Blastn
[2023-06-29 12:30:18,603] [INFO] Running command: blastn -query GCA_021648685.1_ASM2164868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76fc150f-6e33-4f95-975d-47dae4daaee7/dqc_reference/reference_markers_gtdb.fasta -out GCA_021648685.1_ASM2164868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:30:19,826] [INFO] Task succeeded: Blastn
[2023-06-29 12:30:19,832] [INFO] Selected 26 target genomes.
[2023-06-29 12:30:19,832] [INFO] Target genome list was writen to GCA_021648685.1_ASM2164868v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:30:19,841] [INFO] Task started: fastANI
[2023-06-29 12:30:19,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg59da1139-e197-4f7a-839c-ae595bebb9a5/GCA_021648685.1_ASM2164868v1_genomic.fna.gz --refList GCA_021648685.1_ASM2164868v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021648685.1_ASM2164868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:30:33,773] [INFO] Task succeeded: fastANI
[2023-06-29 12:30:33,800] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:30:33,800] [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_015490795.1	s__DRKS01 sp015490795	86.0372	695	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	99.53	99.46	0.94	0.93	5	-
GCA_011051655.1	s__DRKS01 sp011051655	77.2166	227	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016842065.1	s__Thiodiazotropha sp016842065	77.0872	52	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003972985.1	s__Thiolapillus sp003972985	76.75	50	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiolapillus	95.0	99.52	99.52	0.88	0.88	2	-
GCF_001007875.1	s__Sedimenticola thiotaurini	76.7359	86	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390365.1	s__SLIM01 sp011390365	76.7013	65	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__SLIM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003062205.1	s__Sedimenticola_A endophacoides	76.62	83	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola_A	95.0	99.88	99.76	0.97	0.95	6	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	76.4501	61	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCA_003058495.1	s__Thiodiazotropha sp003058495	76.4401	59	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.61	99.54	0.96	0.95	6	-
GCF_000428045.1	s__Sedimenticola selenatireducens	76.4247	91	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	98.15	98.15	0.90	0.90	2	-
GCA_011051715.1	s__HyVt-443 sp011051715	76.3823	92	935	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_003094535.1	s__Thiodiazotropha sp003094535	76.3717	55	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.75	99.58	0.95	0.90	13	-
GCF_001708965.1	s__Thiodiazotropha endoloripes	76.3689	60	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.62	99.43	0.97	0.94	9	-
GCA_019100305.1	s__Thiodiazotropha sp019100305	76.3227	56	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001709035.1	s__Thiodiazotropha endoloripes_B	76.2675	66	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.26	97.31	0.93	0.86	11	-
GCA_003094555.1	s__Thiodiazotropha sp003094555	76.2407	51	935	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.74	99.69	0.92	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-29 12:30:33,803] [INFO] GTDB search result was written to GCA_021648685.1_ASM2164868v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:30:33,803] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:30:33,807] [INFO] DFAST_QC result json was written to GCA_021648685.1_ASM2164868v1_genomic.fna/dqc_result.json
[2023-06-29 12:30:33,807] [INFO] DFAST_QC completed!
[2023-06-29 12:30:33,808] [INFO] Total running time: 0h1m15s