[2023-06-28 16:43:20,995] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:43:20,997] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:43:20,997] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c51286d-7f2e-4e12-abaa-dd536cd60246/dqc_reference
[2023-06-28 16:43:22,222] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:43:22,223] [INFO] Task started: Prodigal
[2023-06-28 16:43:22,224] [INFO] Running command: gunzip -c /var/lib/cwl/stge724b1f7-31a0-42ca-a142-cd80ddb6e642/GCA_017430985.1_ASM1743098v1_genomic.fna.gz | prodigal -d GCA_017430985.1_ASM1743098v1_genomic.fna/cds.fna -a GCA_017430985.1_ASM1743098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:43:26,502] [INFO] Task succeeded: Prodigal
[2023-06-28 16:43:26,502] [INFO] Task started: HMMsearch
[2023-06-28 16:43:26,502] [INFO] Running command: hmmsearch --tblout GCA_017430985.1_ASM1743098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c51286d-7f2e-4e12-abaa-dd536cd60246/dqc_reference/reference_markers.hmm GCA_017430985.1_ASM1743098v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:43:26,729] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:43:26,730] [INFO] Found 6/6 markers.
[2023-06-28 16:43:26,753] [INFO] Query marker FASTA was written to GCA_017430985.1_ASM1743098v1_genomic.fna/markers.fasta
[2023-06-28 16:43:26,753] [INFO] Task started: Blastn
[2023-06-28 16:43:26,753] [INFO] Running command: blastn -query GCA_017430985.1_ASM1743098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c51286d-7f2e-4e12-abaa-dd536cd60246/dqc_reference/reference_markers.fasta -out GCA_017430985.1_ASM1743098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:43:27,435] [INFO] Task succeeded: Blastn
[2023-06-28 16:43:27,439] [INFO] Selected 24 target genomes.
[2023-06-28 16:43:27,440] [INFO] Target genome list was writen to GCA_017430985.1_ASM1743098v1_genomic.fna/target_genomes.txt
[2023-06-28 16:43:27,444] [INFO] Task started: fastANI
[2023-06-28 16:43:27,445] [INFO] Running command: fastANI --query /var/lib/cwl/stge724b1f7-31a0-42ca-a142-cd80ddb6e642/GCA_017430985.1_ASM1743098v1_genomic.fna.gz --refList GCA_017430985.1_ASM1743098v1_genomic.fna/target_genomes.txt --output GCA_017430985.1_ASM1743098v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:43:41,960] [INFO] Task succeeded: fastANI
[2023-06-28 16:43:41,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c51286d-7f2e-4e12-abaa-dd536cd60246/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:43:41,961] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c51286d-7f2e-4e12-abaa-dd536cd60246/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:43:41,974] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:43:41,975] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:43:41,975] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.4674	65	559	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.3659	65	559	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.315	81	559	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.2701	85	559	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.1724	63	559	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.0639	64	559	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.8014	53	559	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	76.7985	58	559	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.7312	59	559	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:43:41,977] [INFO] DFAST Taxonomy check result was written to GCA_017430985.1_ASM1743098v1_genomic.fna/tc_result.tsv
[2023-06-28 16:43:41,977] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:43:41,978] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:43:41,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c51286d-7f2e-4e12-abaa-dd536cd60246/dqc_reference/checkm_data
[2023-06-28 16:43:41,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:43:42,000] [INFO] Task started: CheckM
[2023-06-28 16:43:42,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017430985.1_ASM1743098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017430985.1_ASM1743098v1_genomic.fna/checkm_input GCA_017430985.1_ASM1743098v1_genomic.fna/checkm_result
[2023-06-28 16:44:01,619] [INFO] Task succeeded: CheckM
[2023-06-28 16:44:01,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 10.19%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 16:44:01,649] [INFO] ===== Completeness check finished =====
[2023-06-28 16:44:01,649] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:44:01,650] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017430985.1_ASM1743098v1_genomic.fna/markers.fasta)
[2023-06-28 16:44:01,650] [INFO] Task started: Blastn
[2023-06-28 16:44:01,651] [INFO] Running command: blastn -query GCA_017430985.1_ASM1743098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c51286d-7f2e-4e12-abaa-dd536cd60246/dqc_reference/reference_markers_gtdb.fasta -out GCA_017430985.1_ASM1743098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:44:02,725] [INFO] Task succeeded: Blastn
[2023-06-28 16:44:02,730] [INFO] Selected 13 target genomes.
[2023-06-28 16:44:02,731] [INFO] Target genome list was writen to GCA_017430985.1_ASM1743098v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:44:02,735] [INFO] Task started: fastANI
[2023-06-28 16:44:02,735] [INFO] Running command: fastANI --query /var/lib/cwl/stge724b1f7-31a0-42ca-a142-cd80ddb6e642/GCA_017430985.1_ASM1743098v1_genomic.fna.gz --refList GCA_017430985.1_ASM1743098v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017430985.1_ASM1743098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:44:08,333] [INFO] Task succeeded: fastANI
[2023-06-28 16:44:08,343] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:44:08,344] [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_017430985.1	s__Limivicinus sp017430985	100.0	557	559	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902778115.1	s__Limivicinus sp902778115	81.8207	307	559	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.60	97.29	0.87	0.83	3	-
GCA_017552325.1	s__Limivicinus sp017552325	81.7386	295	559	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801295.1	s__Limivicinus sp902801295	81.5537	265	559	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319465.1	s__Limivicinus sp900319465	81.4645	269	559	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.77	99.67	0.93	0.92	4	-
GCA_902761055.1	s__Limivicinus sp902761055	81.4096	286	559	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319935.1	s__Limivicinus sp900319935	81.3009	277	559	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.02	98.62	0.86	0.80	6	-
GCA_902778285.1	s__Limivicinus sp902778285	81.2646	293	559	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.33	98.33	0.79	0.79	2	-
GCA_905233595.1	s__Limivicinus sp905233595	81.0044	182	559	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785115.1	s__Limivicinus sp902785115	80.3762	202	559	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765595.1	s__Limivicinus sp002350825	80.1129	243	559	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.80	99.80	0.90	0.90	2	-
GCA_017477695.1	s__Limivicinus sp017477695	80.0652	221	559	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:44:08,346] [INFO] GTDB search result was written to GCA_017430985.1_ASM1743098v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:44:08,346] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:44:08,350] [INFO] DFAST_QC result json was written to GCA_017430985.1_ASM1743098v1_genomic.fna/dqc_result.json
[2023-06-28 16:44:08,350] [INFO] DFAST_QC completed!
[2023-06-28 16:44:08,351] [INFO] Total running time: 0h0m47s