[2023-06-04 20:01:51,727] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:01:51,730] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:01:51,730] [INFO] DQC Reference Directory: /var/lib/cwl/stgec5f6cff-5810-43fd-8b90-d5a40ccb7a40/dqc_reference
[2023-06-04 20:01:53,103] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:01:53,104] [INFO] Task started: Prodigal
[2023-06-04 20:01:53,104] [INFO] Running command: gunzip -c /var/lib/cwl/stgc43af5aa-3fd5-43bd-90b7-e2f81c4424f1/GCA_934203155.1_ERR7746111_bin.219_genomic.fna.gz | prodigal -d GCA_934203155.1_ERR7746111_bin.219_genomic.fna/cds.fna -a GCA_934203155.1_ERR7746111_bin.219_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:02:09,084] [INFO] Task succeeded: Prodigal
[2023-06-04 20:02:09,084] [INFO] Task started: HMMsearch
[2023-06-04 20:02:09,085] [INFO] Running command: hmmsearch --tblout GCA_934203155.1_ERR7746111_bin.219_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec5f6cff-5810-43fd-8b90-d5a40ccb7a40/dqc_reference/reference_markers.hmm GCA_934203155.1_ERR7746111_bin.219_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:02:09,282] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:02:09,283] [INFO] Found 6/6 markers.
[2023-06-04 20:02:09,309] [INFO] Query marker FASTA was written to GCA_934203155.1_ERR7746111_bin.219_genomic.fna/markers.fasta
[2023-06-04 20:02:09,310] [INFO] Task started: Blastn
[2023-06-04 20:02:09,310] [INFO] Running command: blastn -query GCA_934203155.1_ERR7746111_bin.219_genomic.fna/markers.fasta -db /var/lib/cwl/stgec5f6cff-5810-43fd-8b90-d5a40ccb7a40/dqc_reference/reference_markers.fasta -out GCA_934203155.1_ERR7746111_bin.219_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:02:09,911] [INFO] Task succeeded: Blastn
[2023-06-04 20:02:09,915] [INFO] Selected 28 target genomes.
[2023-06-04 20:02:09,915] [INFO] Target genome list was writen to GCA_934203155.1_ERR7746111_bin.219_genomic.fna/target_genomes.txt
[2023-06-04 20:02:09,919] [INFO] Task started: fastANI
[2023-06-04 20:02:09,919] [INFO] Running command: fastANI --query /var/lib/cwl/stgc43af5aa-3fd5-43bd-90b7-e2f81c4424f1/GCA_934203155.1_ERR7746111_bin.219_genomic.fna.gz --refList GCA_934203155.1_ERR7746111_bin.219_genomic.fna/target_genomes.txt --output GCA_934203155.1_ERR7746111_bin.219_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:02:22,740] [INFO] Task succeeded: fastANI
[2023-06-04 20:02:22,740] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec5f6cff-5810-43fd-8b90-d5a40ccb7a40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:02:22,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec5f6cff-5810-43fd-8b90-d5a40ccb7a40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:02:22,758] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:02:22,758] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 20:02:22,758] [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 pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.6328	124	860	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.557	189	860	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	77.2035	163	860	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.1001	52	860	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.0918	138	860	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.0807	169	860	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	77.0804	171	860	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	77.0504	53	860	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	77.0321	174	860	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.9716	93	860	95	below_threshold
Prevotella fusca	strain=JCM 17724	GCA_000614245.1	589436	589436	type	True	76.9116	75	860	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.8769	77	860	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.8125	78	860	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.6583	108	860	95	below_threshold
Prevotella enoeca	strain=JCM 12259	GCA_000613405.1	76123	76123	type	True	76.5769	53	860	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.5241	92	860	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	76.4637	70	860	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	76.4355	71	860	95	below_threshold
Prevotella shahii	strain=DSM 15611	GCA_003201715.1	228603	228603	type	True	76.4225	53	860	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 20:02:22,761] [INFO] DFAST Taxonomy check result was written to GCA_934203155.1_ERR7746111_bin.219_genomic.fna/tc_result.tsv
[2023-06-04 20:02:22,762] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:02:22,762] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:02:22,762] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec5f6cff-5810-43fd-8b90-d5a40ccb7a40/dqc_reference/checkm_data
[2023-06-04 20:02:22,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:02:22,792] [INFO] Task started: CheckM
[2023-06-04 20:02:22,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934203155.1_ERR7746111_bin.219_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934203155.1_ERR7746111_bin.219_genomic.fna/checkm_input GCA_934203155.1_ERR7746111_bin.219_genomic.fna/checkm_result
[2023-06-04 20:03:07,919] [INFO] Task succeeded: CheckM
[2023-06-04 20:03:07,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:03:07,942] [INFO] ===== Completeness check finished =====
[2023-06-04 20:03:07,942] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:03:07,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934203155.1_ERR7746111_bin.219_genomic.fna/markers.fasta)
[2023-06-04 20:03:07,943] [INFO] Task started: Blastn
[2023-06-04 20:03:07,943] [INFO] Running command: blastn -query GCA_934203155.1_ERR7746111_bin.219_genomic.fna/markers.fasta -db /var/lib/cwl/stgec5f6cff-5810-43fd-8b90-d5a40ccb7a40/dqc_reference/reference_markers_gtdb.fasta -out GCA_934203155.1_ERR7746111_bin.219_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:03:08,833] [INFO] Task succeeded: Blastn
[2023-06-04 20:03:08,837] [INFO] Selected 25 target genomes.
[2023-06-04 20:03:08,837] [INFO] Target genome list was writen to GCA_934203155.1_ERR7746111_bin.219_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:03:08,864] [INFO] Task started: fastANI
[2023-06-04 20:03:08,864] [INFO] Running command: fastANI --query /var/lib/cwl/stgc43af5aa-3fd5-43bd-90b7-e2f81c4424f1/GCA_934203155.1_ERR7746111_bin.219_genomic.fna.gz --refList GCA_934203155.1_ERR7746111_bin.219_genomic.fna/target_genomes_gtdb.txt --output GCA_934203155.1_ERR7746111_bin.219_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:03:22,683] [INFO] Task succeeded: fastANI
[2023-06-04 20:03:22,703] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:03:22,703] [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
GCF_002251385.1	s__Prevotella sp002251385	97.1588	778	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.22	97.07	0.92	0.88	8	conclusive
GCA_004554665.1	s__Prevotella sp004554665	78.3336	243	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002265625.1	s__Prevotella sp002265625	77.7067	176	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.80	0.88	0.86	4	-
GCF_002251365.1	s__Prevotella sp002251365	77.5066	144	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.20	97.97	0.85	0.80	5	-
GCA_900544495.1	s__Prevotella sp900544495	77.464	167	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_002439605.1	s__Prevotella sp002439605	77.3466	99	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.57	99.57	0.81	0.81	2	-
GCA_900543975.1	s__Prevotella sp900543975	77.3234	163	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.48	97.34	0.84	0.79	5	-
GCA_900199655.1	s__Prevotella sp900199655	77.2122	188	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.91	99.91	0.98	0.98	2	-
GCA_900546575.1	s__Prevotella sp900546575	77.1247	173	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCF_000184945.1	s__Prevotella buccae	77.0918	138	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCF_018789675.1	s__Prevotella sp002300055	77.0807	169	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.15	99.02	0.92	0.90	6	-
GCA_900319905.1	s__Prevotella sp900319905	77.0208	120	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.87	98.44	0.89	0.87	7	-
GCA_900546345.1	s__Prevotella sp900546345	76.9705	97	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900555035.1	s__Prevotella sp900555035	76.9016	115	860	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	76.8808	95	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.60	0.86	0.83	10	-
GCA_900317305.1	s__Prevotella sp900317305	76.7981	156	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	97.82	0.87	0.83	11	-
GCA_905234355.1	s__Prevotella sp905234355	76.7969	120	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548535.1	s__Prevotella sp900548535	76.7704	119	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017476785.1	s__Prevotella sp017476785	76.7036	132	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315455.1	s__Prevotella sp900315455	76.6648	135	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.41	96.59	0.90	0.86	13	-
GCA_017557405.1	s__Prevotella sp017557405	76.6292	117	860	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	76.5241	92	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.93	99.88	0.98	0.97	6	-
GCA_000435635.1	s__Prevotella avicola	76.4	108	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.53	97.19	0.88	0.87	5	-
GCA_902784065.1	s__Prevotella sp902784065	76.3769	78	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902770195.1	s__Prevotella sp902770195	76.2815	75	860	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 20:03:22,706] [INFO] GTDB search result was written to GCA_934203155.1_ERR7746111_bin.219_genomic.fna/result_gtdb.tsv
[2023-06-04 20:03:22,707] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:03:22,712] [INFO] DFAST_QC result json was written to GCA_934203155.1_ERR7746111_bin.219_genomic.fna/dqc_result.json
[2023-06-04 20:03:22,712] [INFO] DFAST_QC completed!
[2023-06-04 20:03:22,712] [INFO] Total running time: 0h1m31s