[2023-06-28 11:34:14,545] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:34:14,547] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:34:14,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg18aa7620-5eed-4588-b666-95f67794aa13/dqc_reference
[2023-06-28 11:34:15,653] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:34:15,653] [INFO] Task started: Prodigal
[2023-06-28 11:34:15,654] [INFO] Running command: gunzip -c /var/lib/cwl/stg56ab6394-462b-46c7-9b7e-ed22a19bf357/GCA_017521045.1_ASM1752104v1_genomic.fna.gz | prodigal -d GCA_017521045.1_ASM1752104v1_genomic.fna/cds.fna -a GCA_017521045.1_ASM1752104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:34:30,160] [INFO] Task succeeded: Prodigal
[2023-06-28 11:34:30,160] [INFO] Task started: HMMsearch
[2023-06-28 11:34:30,160] [INFO] Running command: hmmsearch --tblout GCA_017521045.1_ASM1752104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18aa7620-5eed-4588-b666-95f67794aa13/dqc_reference/reference_markers.hmm GCA_017521045.1_ASM1752104v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:34:30,353] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:34:30,354] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg56ab6394-462b-46c7-9b7e-ed22a19bf357/GCA_017521045.1_ASM1752104v1_genomic.fna.gz]
[2023-06-28 11:34:30,380] [INFO] Query marker FASTA was written to GCA_017521045.1_ASM1752104v1_genomic.fna/markers.fasta
[2023-06-28 11:34:30,381] [INFO] Task started: Blastn
[2023-06-28 11:34:30,381] [INFO] Running command: blastn -query GCA_017521045.1_ASM1752104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18aa7620-5eed-4588-b666-95f67794aa13/dqc_reference/reference_markers.fasta -out GCA_017521045.1_ASM1752104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:34:30,930] [INFO] Task succeeded: Blastn
[2023-06-28 11:34:30,933] [INFO] Selected 25 target genomes.
[2023-06-28 11:34:30,933] [INFO] Target genome list was writen to GCA_017521045.1_ASM1752104v1_genomic.fna/target_genomes.txt
[2023-06-28 11:34:30,939] [INFO] Task started: fastANI
[2023-06-28 11:34:30,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg56ab6394-462b-46c7-9b7e-ed22a19bf357/GCA_017521045.1_ASM1752104v1_genomic.fna.gz --refList GCA_017521045.1_ASM1752104v1_genomic.fna/target_genomes.txt --output GCA_017521045.1_ASM1752104v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:34:42,420] [INFO] Task succeeded: fastANI
[2023-06-28 11:34:42,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18aa7620-5eed-4588-b666-95f67794aa13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:34:42,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18aa7620-5eed-4588-b666-95f67794aa13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:34:42,431] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 11:34:42,431] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 11:34:42,431] [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
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.6912	91	1083	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	77.6385	68	1083	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.6219	67	1083	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.4032	96	1083	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.3987	99	1083	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.3581	95	1083	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.2667	105	1083	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	77.18	120	1083	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	77.1782	118	1083	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.9946	136	1083	95	below_threshold
Prevotella paludivivens	strain=JCM 13650	GCA_000613605.1	185294	185294	type	True	76.8543	52	1083	95	below_threshold
Prevotella bryantii	strain=DSM 11371	GCA_019973295.1	77095	77095	type	True	76.8203	57	1083	95	below_threshold
Prevotella paludivivens	strain=DSM 17968	GCA_000373185.1	185294	185294	type	True	76.8072	53	1083	95	below_threshold
Prevotella bryantii	strain=B14	GCA_022024235.1	77095	77095	type	True	76.7591	56	1083	95	below_threshold
Prevotella oryzae	strain=DSM 17970	GCA_000585355.1	185293	185293	type	True	76.7523	60	1083	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	76.6559	114	1083	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 11:34:42,432] [INFO] DFAST Taxonomy check result was written to GCA_017521045.1_ASM1752104v1_genomic.fna/tc_result.tsv
[2023-06-28 11:34:42,433] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:34:42,433] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:34:42,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18aa7620-5eed-4588-b666-95f67794aa13/dqc_reference/checkm_data
[2023-06-28 11:34:42,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:34:42,468] [INFO] Task started: CheckM
[2023-06-28 11:34:42,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017521045.1_ASM1752104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017521045.1_ASM1752104v1_genomic.fna/checkm_input GCA_017521045.1_ASM1752104v1_genomic.fna/checkm_result
[2023-06-28 11:35:25,101] [INFO] Task succeeded: CheckM
[2023-06-28 11:35:25,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 12.50%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-28 11:35:25,121] [INFO] ===== Completeness check finished =====
[2023-06-28 11:35:25,121] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:35:25,122] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017521045.1_ASM1752104v1_genomic.fna/markers.fasta)
[2023-06-28 11:35:25,122] [INFO] Task started: Blastn
[2023-06-28 11:35:25,122] [INFO] Running command: blastn -query GCA_017521045.1_ASM1752104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18aa7620-5eed-4588-b666-95f67794aa13/dqc_reference/reference_markers_gtdb.fasta -out GCA_017521045.1_ASM1752104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:35:25,955] [INFO] Task succeeded: Blastn
[2023-06-28 11:35:25,958] [INFO] Selected 24 target genomes.
[2023-06-28 11:35:25,958] [INFO] Target genome list was writen to GCA_017521045.1_ASM1752104v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:35:25,972] [INFO] Task started: fastANI
[2023-06-28 11:35:25,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg56ab6394-462b-46c7-9b7e-ed22a19bf357/GCA_017521045.1_ASM1752104v1_genomic.fna.gz --refList GCA_017521045.1_ASM1752104v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017521045.1_ASM1752104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:35:39,146] [INFO] Task succeeded: fastANI
[2023-06-28 11:35:39,159] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 11:35:39,160] [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_017410365.1	s__Prevotella sp017410365	97.1138	871	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.93	96.60	0.79	0.74	5	conclusive
GCA_017415455.1	s__Prevotella sp017415455	81.208	180	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.31	98.11	0.83	0.82	3	-
GCA_017483185.1	s__Prevotella sp017483185	77.6008	96	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100635.1	s__Prevotella sp900100635	77.5948	111	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.60	0.86	0.83	10	-
GCF_015074785.1	s__Prevotella sp015074785	77.5111	91	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCF_000834015.1	s__Prevotella pectinovora	77.2891	104	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.37	97.34	0.86	0.79	12	-
GCA_002314055.1	s__Prevotella sp002314055	77.2524	94	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.08	98.98	0.90	0.84	9	-
GCA_900770395.1	s__Prevotella sp900770395	77.2503	122	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.78	95.78	0.79	0.79	2	-
GCF_002933775.1	s__Prevotella sp002933775	77.1781	106	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.87	97.52	0.85	0.83	11	-
GCF_016899955.1	s__Prevotella sp900540415	77.1002	111	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	98.08	0.94	0.91	6	-
GCA_900557255.1	s__Prevotella sp900557255	77.053	51	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013166545.1	s__Prevotella sp013166545	76.9666	132	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.93	99.88	0.98	0.97	6	-
GCA_900549175.1	s__Prevotella sp900549175	76.9591	121	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.84	99.84	0.89	0.89	2	-
GCA_017458005.1	s__Prevotella sp017458005	76.8897	101	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.28	97.28	0.86	0.86	2	-
GCA_905233985.1	s__Prevotella sp905233985	76.7913	82	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543975.1	s__Prevotella sp900543975	76.7372	77	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.48	97.34	0.84	0.79	5	-
GCA_905233825.1	s__Prevotella sp905233825	76.4843	95	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798425.1	s__Prevotella sp902798425	76.4045	100	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.06	97.06	0.85	0.85	2	-
GCA_017645905.1	s__Prevotella sp017645905	76.3982	78	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017400455.1	s__Prevotella sp017400455	76.3295	60	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017474515.1	s__Prevotella sp017474515	76.1591	73	1083	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 11:35:39,161] [INFO] GTDB search result was written to GCA_017521045.1_ASM1752104v1_genomic.fna/result_gtdb.tsv
[2023-06-28 11:35:39,162] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:35:39,165] [INFO] DFAST_QC result json was written to GCA_017521045.1_ASM1752104v1_genomic.fna/dqc_result.json
[2023-06-28 11:35:39,165] [INFO] DFAST_QC completed!
[2023-06-28 11:35:39,165] [INFO] Total running time: 0h1m25s