[2023-06-28 19:04:10,517] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:04:10,519] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:04:10,520] [INFO] DQC Reference Directory: /var/lib/cwl/stgad6f6379-18f7-4870-aa2a-1f054add2c93/dqc_reference
[2023-06-28 19:04:11,780] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:04:11,781] [INFO] Task started: Prodigal
[2023-06-28 19:04:11,781] [INFO] Running command: gunzip -c /var/lib/cwl/stga058f504-2f6f-49c9-84ff-bf77481ba3d5/GCA_017477245.1_ASM1747724v1_genomic.fna.gz | prodigal -d GCA_017477245.1_ASM1747724v1_genomic.fna/cds.fna -a GCA_017477245.1_ASM1747724v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:04:25,016] [INFO] Task succeeded: Prodigal
[2023-06-28 19:04:25,017] [INFO] Task started: HMMsearch
[2023-06-28 19:04:25,017] [INFO] Running command: hmmsearch --tblout GCA_017477245.1_ASM1747724v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad6f6379-18f7-4870-aa2a-1f054add2c93/dqc_reference/reference_markers.hmm GCA_017477245.1_ASM1747724v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:04:25,256] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:04:25,258] [INFO] Found 6/6 markers.
[2023-06-28 19:04:25,281] [INFO] Query marker FASTA was written to GCA_017477245.1_ASM1747724v1_genomic.fna/markers.fasta
[2023-06-28 19:04:25,282] [INFO] Task started: Blastn
[2023-06-28 19:04:25,282] [INFO] Running command: blastn -query GCA_017477245.1_ASM1747724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad6f6379-18f7-4870-aa2a-1f054add2c93/dqc_reference/reference_markers.fasta -out GCA_017477245.1_ASM1747724v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:04:25,972] [INFO] Task succeeded: Blastn
[2023-06-28 19:04:25,976] [INFO] Selected 33 target genomes.
[2023-06-28 19:04:25,977] [INFO] Target genome list was writen to GCA_017477245.1_ASM1747724v1_genomic.fna/target_genomes.txt
[2023-06-28 19:04:25,980] [INFO] Task started: fastANI
[2023-06-28 19:04:25,980] [INFO] Running command: fastANI --query /var/lib/cwl/stga058f504-2f6f-49c9-84ff-bf77481ba3d5/GCA_017477245.1_ASM1747724v1_genomic.fna.gz --refList GCA_017477245.1_ASM1747724v1_genomic.fna/target_genomes.txt --output GCA_017477245.1_ASM1747724v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:04:48,261] [INFO] Task succeeded: fastANI
[2023-06-28 19:04:48,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad6f6379-18f7-4870-aa2a-1f054add2c93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:04:48,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad6f6379-18f7-4870-aa2a-1f054add2c93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:04:48,274] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:04:48,274] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:04:48,274] [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
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	76.9568	73	770	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	76.954	71	770	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	76.3189	57	770	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	76.2855	58	770	95	below_threshold
Alistipes megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	76.2227	65	770	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	76.1893	63	770	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	76.105	64	770	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	75.8432	57	770	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	74.9827	53	770	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	74.9363	56	770	95	below_threshold
Corallococcus carmarthensis	strain=CA043D	GCA_003611695.1	2316728	2316728	type	True	74.8944	53	770	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	74.8941	54	770	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	74.8828	56	770	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.6608	59	770	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:04:48,276] [INFO] DFAST Taxonomy check result was written to GCA_017477245.1_ASM1747724v1_genomic.fna/tc_result.tsv
[2023-06-28 19:04:48,277] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:04:48,277] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:04:48,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad6f6379-18f7-4870-aa2a-1f054add2c93/dqc_reference/checkm_data
[2023-06-28 19:04:48,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:04:48,307] [INFO] Task started: CheckM
[2023-06-28 19:04:48,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017477245.1_ASM1747724v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017477245.1_ASM1747724v1_genomic.fna/checkm_input GCA_017477245.1_ASM1747724v1_genomic.fna/checkm_result
[2023-06-28 19:05:26,934] [INFO] Task succeeded: CheckM
[2023-06-28 19:05:26,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 19:05:26,959] [INFO] ===== Completeness check finished =====
[2023-06-28 19:05:26,959] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:05:26,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017477245.1_ASM1747724v1_genomic.fna/markers.fasta)
[2023-06-28 19:05:26,960] [INFO] Task started: Blastn
[2023-06-28 19:05:26,960] [INFO] Running command: blastn -query GCA_017477245.1_ASM1747724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad6f6379-18f7-4870-aa2a-1f054add2c93/dqc_reference/reference_markers_gtdb.fasta -out GCA_017477245.1_ASM1747724v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:05:27,988] [INFO] Task succeeded: Blastn
[2023-06-28 19:05:27,993] [INFO] Selected 19 target genomes.
[2023-06-28 19:05:27,993] [INFO] Target genome list was writen to GCA_017477245.1_ASM1747724v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:05:27,996] [INFO] Task started: fastANI
[2023-06-28 19:05:27,996] [INFO] Running command: fastANI --query /var/lib/cwl/stga058f504-2f6f-49c9-84ff-bf77481ba3d5/GCA_017477245.1_ASM1747724v1_genomic.fna.gz --refList GCA_017477245.1_ASM1747724v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017477245.1_ASM1747724v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:05:37,291] [INFO] Task succeeded: fastANI
[2023-06-28 19:05:37,319] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:05:37,320] [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_017477245.1	s__Cryptobacteroides sp017477245	100.0	768	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.05	97.38	0.81	0.78	3	conclusive
GCA_017428725.1	s__Cryptobacteroides sp017428725	86.9742	557	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.64	97.64	0.87	0.87	2	-
GCA_017454905.1	s__Cryptobacteroides sp017454905	85.1247	487	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458145.1	s__Cryptobacteroides sp017458145	85.0915	452	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319975.1	s__Cryptobacteroides sp900319975	84.9986	369	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.34	97.18	0.88	0.88	3	-
GCA_016290835.1	s__Cryptobacteroides sp016290835	84.8327	520	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900167895.1	s__Cryptobacteroides sp900167895	84.6909	415	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.90	0.94	0.93	3	-
GCA_902768985.1	s__Cryptobacteroides sp902768985	84.6346	409	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.65	98.07	0.93	0.92	5	-
GCA_902790635.1	s__Cryptobacteroides sp902790635	84.4238	434	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902762435.1	s__Cryptobacteroides sp902762435	84.3552	411	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.59	98.59	0.91	0.91	2	-
GCA_902789245.1	s__Cryptobacteroides sp902789245	84.324	390	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.35	96.71	0.87	0.86	3	-
GCA_017960585.1	s__Cryptobacteroides sp017960585	84.2882	367	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234475.1	s__Cryptobacteroides sp905234475	84.1663	388	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235775.1	s__Cryptobacteroides sp905235775	83.8657	309	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798975.1	s__Cryptobacteroides sp902798975	83.7728	354	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017548445.1	s__Cryptobacteroides sp017548445	83.7115	324	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016291185.1	s__Cryptobacteroides sp016291185	83.6191	352	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001602885.1	s__Cryptobacteroides sp001602885	83.6099	210	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744435.1	s__Cryptobacteroides sp012744435	83.5591	375	770	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:05:37,323] [INFO] GTDB search result was written to GCA_017477245.1_ASM1747724v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:05:37,324] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:05:37,330] [INFO] DFAST_QC result json was written to GCA_017477245.1_ASM1747724v1_genomic.fna/dqc_result.json
[2023-06-28 19:05:37,330] [INFO] DFAST_QC completed!
[2023-06-28 19:05:37,330] [INFO] Total running time: 0h1m27s