[2023-06-08 20:36:25,720] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:36:25,724] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:36:25,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg28f54412-3b42-4f28-91e2-098d006501bd/dqc_reference
[2023-06-08 20:36:28,107] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:36:28,108] [INFO] Task started: Prodigal
[2023-06-08 20:36:28,108] [INFO] Running command: gunzip -c /var/lib/cwl/stg307ae599-cad5-4470-b03a-9e4df8e5ff0c/GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:36:42,640] [INFO] Task succeeded: Prodigal
[2023-06-08 20:36:42,641] [INFO] Task started: HMMsearch
[2023-06-08 20:36:42,641] [INFO] Running command: hmmsearch --tblout GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28f54412-3b42-4f28-91e2-098d006501bd/dqc_reference/reference_markers.hmm GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:36:42,859] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:36:42,860] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg307ae599-cad5-4470-b03a-9e4df8e5ff0c/GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 20:36:42,883] [INFO] Query marker FASTA was written to GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 20:36:42,884] [INFO] Task started: Blastn
[2023-06-08 20:36:42,884] [INFO] Running command: blastn -query GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg28f54412-3b42-4f28-91e2-098d006501bd/dqc_reference/reference_markers.fasta -out GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:36:43,497] [INFO] Task succeeded: Blastn
[2023-06-08 20:36:43,501] [INFO] Selected 26 target genomes.
[2023-06-08 20:36:43,502] [INFO] Target genome list was writen to GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 20:36:43,502] [INFO] Task started: fastANI
[2023-06-08 20:36:43,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg307ae599-cad5-4470-b03a-9e4df8e5ff0c/GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:36:55,274] [INFO] Task succeeded: fastANI
[2023-06-08 20:36:55,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28f54412-3b42-4f28-91e2-098d006501bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:36:55,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28f54412-3b42-4f28-91e2-098d006501bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:36:55,290] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:36:55,290] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:36:55,290] [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	77.9748	143	599	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	77.0493	66	599	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.6105	84	599	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.4998	111	599	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.47	108	599	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.4463	110	599	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.4217	111	599	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.406	112	599	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.371	73	599	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.3315	99	599	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.29	83	599	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.2302	86	599	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:36:55,292] [INFO] DFAST Taxonomy check result was written to GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 20:36:55,293] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:36:55,293] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:36:55,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28f54412-3b42-4f28-91e2-098d006501bd/dqc_reference/checkm_data
[2023-06-08 20:36:55,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:36:55,316] [INFO] Task started: CheckM
[2023-06-08 20:36:55,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 20:37:39,630] [INFO] Task succeeded: CheckM
[2023-06-08 20:37:39,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.63%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:37:39,652] [INFO] ===== Completeness check finished =====
[2023-06-08 20:37:39,652] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:37:39,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 20:37:39,653] [INFO] Task started: Blastn
[2023-06-08 20:37:39,653] [INFO] Running command: blastn -query GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg28f54412-3b42-4f28-91e2-098d006501bd/dqc_reference/reference_markers_gtdb.fasta -out GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:37:40,563] [INFO] Task succeeded: Blastn
[2023-06-08 20:37:40,567] [INFO] Selected 22 target genomes.
[2023-06-08 20:37:40,568] [INFO] Target genome list was writen to GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:37:40,569] [INFO] Task started: fastANI
[2023-06-08 20:37:40,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg307ae599-cad5-4470-b03a-9e4df8e5ff0c/GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:37:50,945] [INFO] Task succeeded: fastANI
[2023-06-08 20:37:50,966] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:37:50,967] [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_004557285.1	s__Prevotella sp004557285	98.6003	455	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.35	98.35	0.77	0.77	2	conclusive
GCA_905214625.1	s__Prevotella sp905214625	77.4994	125	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016302965.1	s__Prevotella sp016302965	77.3844	138	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001275135.1	s__Prevotella rara	77.3539	162	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.17	97.70	0.90	0.86	7	-
GCA_905215655.1	s__Prevotella sp905215655	77.3019	103	599	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	77.2398	151	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.53	95.99	0.92	0.86	5	-
GCA_900318915.1	s__Prevotella sp900318915	77.0567	137	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.05	95.26	0.87	0.81	11	-
GCA_002369515.1	s__Prevotella sp002369515	77.0407	125	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767775.1	s__Prevotella sp902767775	77.0275	119	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.97	97.97	0.86	0.86	2	-
GCA_002353525.1	s__Prevotella sp002353525	76.9655	114	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795605.1	s__Prevotella sp902795605	76.819	135	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905211345.1	s__Prevotella sp905211345	76.7455	87	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550365.1	s__Prevotella sp900550365	76.7427	116	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016901395.1	s__Prevotella sp016901395	76.7418	98	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545525.1	s__Prevotella sp900545525	76.7146	124	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.81	98.33	0.87	0.76	5	-
GCF_016899855.1	s__Prevotella sp000436595	76.5126	120	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.00	97.50	0.84	0.81	5	-
GCF_018789675.1	s__Prevotella sp002300055	76.4691	110	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.15	99.02	0.92	0.90	6	-
GCF_013166515.1	s__Prevotella sp013166515	76.409	114	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.36	96.74	0.93	0.86	3	-
GCA_002437285.1	s__Prevotella sp002437285	76.4015	87	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.68	99.38	0.93	0.88	13	-
GCA_900762125.1	s__Prevotella sp900762125	76.3797	80	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016291915.1	s__Prevotella sp016291915	76.0016	56	599	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 20:37:50,969] [INFO] GTDB search result was written to GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 20:37:50,969] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:37:50,973] [INFO] DFAST_QC result json was written to GCA_945831775.1_SRR5976182_bin.2_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 20:37:50,973] [INFO] DFAST_QC completed!
[2023-06-08 20:37:50,974] [INFO] Total running time: 0h1m25s