[2023-06-28 16:34:00,803] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:34:00,805] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:34:00,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg6296677f-1ec4-4de1-90a9-ef2dfd48a5b0/dqc_reference
[2023-06-28 16:34:02,008] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:34:02,008] [INFO] Task started: Prodigal
[2023-06-28 16:34:02,009] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9b5848b-71e9-4ebd-84d0-c799168a2bb0/GCA_944321665.1_BRZ_PQ_bin6_genomic.fna.gz | prodigal -d GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/cds.fna -a GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:34:17,592] [INFO] Task succeeded: Prodigal
[2023-06-28 16:34:17,592] [INFO] Task started: HMMsearch
[2023-06-28 16:34:17,592] [INFO] Running command: hmmsearch --tblout GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6296677f-1ec4-4de1-90a9-ef2dfd48a5b0/dqc_reference/reference_markers.hmm GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:34:17,769] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:34:17,770] [INFO] Found 6/6 markers.
[2023-06-28 16:34:17,795] [INFO] Query marker FASTA was written to GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/markers.fasta
[2023-06-28 16:34:17,796] [INFO] Task started: Blastn
[2023-06-28 16:34:17,796] [INFO] Running command: blastn -query GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/markers.fasta -db /var/lib/cwl/stg6296677f-1ec4-4de1-90a9-ef2dfd48a5b0/dqc_reference/reference_markers.fasta -out GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:34:18,387] [INFO] Task succeeded: Blastn
[2023-06-28 16:34:18,391] [INFO] Selected 27 target genomes.
[2023-06-28 16:34:18,392] [INFO] Target genome list was writen to GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/target_genomes.txt
[2023-06-28 16:34:18,394] [INFO] Task started: fastANI
[2023-06-28 16:34:18,394] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9b5848b-71e9-4ebd-84d0-c799168a2bb0/GCA_944321665.1_BRZ_PQ_bin6_genomic.fna.gz --refList GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/target_genomes.txt --output GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:34:30,924] [INFO] Task succeeded: fastANI
[2023-06-28 16:34:30,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6296677f-1ec4-4de1-90a9-ef2dfd48a5b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:34:30,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6296677f-1ec4-4de1-90a9-ef2dfd48a5b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:34:30,940] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:34:30,941] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:34:30,941] [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	77.6361	121	932	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.2752	141	932	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	77.2439	82	932	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.1685	137	932	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	77.1527	120	932	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	77.0594	84	932	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.9759	72	932	95	below_threshold
Prevotella oris	strain=JCM 12252	GCA_000613505.1	28135	28135	type	True	76.8982	50	932	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	76.8316	69	932	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.8128	66	932	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.4822	91	932	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.4558	80	932	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	76.3931	58	932	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	76.3596	60	932	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.3505	77	932	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	76.3051	71	932	95	below_threshold
Prevotella koreensis	strain=KCOM 3155	GCA_003977605.1	2490854	2490854	type	True	76.2485	65	932	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	76.1151	73	932	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:34:30,943] [INFO] DFAST Taxonomy check result was written to GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/tc_result.tsv
[2023-06-28 16:34:30,944] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:34:30,944] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:34:30,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6296677f-1ec4-4de1-90a9-ef2dfd48a5b0/dqc_reference/checkm_data
[2023-06-28 16:34:30,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:34:30,974] [INFO] Task started: CheckM
[2023-06-28 16:34:30,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/checkm_input GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/checkm_result
[2023-06-28 16:35:14,798] [INFO] Task succeeded: CheckM
[2023-06-28 16:35:14,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:35:14,818] [INFO] ===== Completeness check finished =====
[2023-06-28 16:35:14,819] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:35:14,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/markers.fasta)
[2023-06-28 16:35:14,819] [INFO] Task started: Blastn
[2023-06-28 16:35:14,819] [INFO] Running command: blastn -query GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/markers.fasta -db /var/lib/cwl/stg6296677f-1ec4-4de1-90a9-ef2dfd48a5b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:35:15,611] [INFO] Task succeeded: Blastn
[2023-06-28 16:35:15,615] [INFO] Selected 16 target genomes.
[2023-06-28 16:35:15,615] [INFO] Target genome list was writen to GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:35:15,617] [INFO] Task started: fastANI
[2023-06-28 16:35:15,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9b5848b-71e9-4ebd-84d0-c799168a2bb0/GCA_944321665.1_BRZ_PQ_bin6_genomic.fna.gz --refList GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/target_genomes_gtdb.txt --output GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:35:23,636] [INFO] Task succeeded: fastANI
[2023-06-28 16:35:23,650] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:35:23,650] [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_000433175.1	s__Prevotella sp000433175	98.3231	759	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.10	97.93	0.86	0.84	3	conclusive
GCA_900554545.1	s__Prevotella sp900554545	80.0274	299	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.93	97.89	0.89	0.88	3	-
GCA_905211345.1	s__Prevotella sp905211345	80.0256	235	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905196835.1	s__Prevotella stercoripullorum	79.9199	369	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.53	95.99	0.92	0.86	5	-
GCF_016899855.1	s__Prevotella sp000436595	79.8779	338	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.00	97.50	0.84	0.81	5	-
GCA_900550365.1	s__Prevotella sp900550365	79.7273	327	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551055.1	s__Prevotella sp900551055	79.5691	341	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.16	98.15	0.84	0.84	3	-
GCA_900554695.1	s__Prevotella sp900554695	77.9927	128	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.93	97.88	0.84	0.83	3	-
GCF_013166515.1	s__Prevotella sp013166515	77.5616	168	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.36	96.74	0.93	0.86	3	-
GCA_002314055.1	s__Prevotella sp002314055	77.4146	107	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.08	98.98	0.90	0.84	9	-
GCA_900545525.1	s__Prevotella sp900545525	77.3692	185	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.81	98.33	0.87	0.76	5	-
GCF_000834015.1	s__Prevotella pectinovora	77.1579	136	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.37	97.34	0.86	0.79	12	-
GCA_900553465.1	s__Prevotella sp900553465	77.0269	106	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.76	96.76	0.80	0.80	2	-
GCA_902801375.1	s__Prevotella sp902801375	76.735	82	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.75	97.75	0.82	0.82	2	-
GCA_900548745.1	s__Prevotella sp900548745	76.6137	90	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.94	97.91	0.83	0.71	3	-
GCA_002299635.1	s__Prevotella sp002299635	76.3757	51	932	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.50	98.47	0.80	0.78	3	-
--------------------------------------------------------------------------------
[2023-06-28 16:35:23,652] [INFO] GTDB search result was written to GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/result_gtdb.tsv
[2023-06-28 16:35:23,653] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:35:23,657] [INFO] DFAST_QC result json was written to GCA_944321665.1_BRZ_PQ_bin6_genomic.fna/dqc_result.json
[2023-06-28 16:35:23,657] [INFO] DFAST_QC completed!
[2023-06-28 16:35:23,657] [INFO] Total running time: 0h1m23s