[2023-06-30 14:48:12,381] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:48:12,383] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:48:12,383] [INFO] DQC Reference Directory: /var/lib/cwl/stg6121b8ab-af60-4648-904d-31d3cc13597f/dqc_reference
[2023-06-30 14:48:13,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:48:13,729] [INFO] Task started: Prodigal
[2023-06-30 14:48:13,729] [INFO] Running command: gunzip -c /var/lib/cwl/stgf972c46c-7443-4370-bfcb-7b9a96b64e8d/GCA_016292545.1_ASM1629254v1_genomic.fna.gz | prodigal -d GCA_016292545.1_ASM1629254v1_genomic.fna/cds.fna -a GCA_016292545.1_ASM1629254v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:48:31,371] [INFO] Task succeeded: Prodigal
[2023-06-30 14:48:31,371] [INFO] Task started: HMMsearch
[2023-06-30 14:48:31,372] [INFO] Running command: hmmsearch --tblout GCA_016292545.1_ASM1629254v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6121b8ab-af60-4648-904d-31d3cc13597f/dqc_reference/reference_markers.hmm GCA_016292545.1_ASM1629254v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:48:31,614] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:48:31,615] [INFO] Found 6/6 markers.
[2023-06-30 14:48:31,700] [INFO] Query marker FASTA was written to GCA_016292545.1_ASM1629254v1_genomic.fna/markers.fasta
[2023-06-30 14:48:31,701] [INFO] Task started: Blastn
[2023-06-30 14:48:31,701] [INFO] Running command: blastn -query GCA_016292545.1_ASM1629254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6121b8ab-af60-4648-904d-31d3cc13597f/dqc_reference/reference_markers.fasta -out GCA_016292545.1_ASM1629254v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:48:32,415] [INFO] Task succeeded: Blastn
[2023-06-30 14:48:32,419] [INFO] Selected 29 target genomes.
[2023-06-30 14:48:32,419] [INFO] Target genome list was writen to GCA_016292545.1_ASM1629254v1_genomic.fna/target_genomes.txt
[2023-06-30 14:48:32,422] [INFO] Task started: fastANI
[2023-06-30 14:48:32,422] [INFO] Running command: fastANI --query /var/lib/cwl/stgf972c46c-7443-4370-bfcb-7b9a96b64e8d/GCA_016292545.1_ASM1629254v1_genomic.fna.gz --refList GCA_016292545.1_ASM1629254v1_genomic.fna/target_genomes.txt --output GCA_016292545.1_ASM1629254v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:48:48,047] [INFO] Task succeeded: fastANI
[2023-06-30 14:48:48,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6121b8ab-af60-4648-904d-31d3cc13597f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:48:48,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6121b8ab-af60-4648-904d-31d3cc13597f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:48:48,054] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:48:48,055] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:48:48,055] [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 dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.4597	79	744	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.4597	79	744	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.4114	76	744	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.2788	64	744	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.2775	57	744	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.2207	60	744	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:48:48,057] [INFO] DFAST Taxonomy check result was written to GCA_016292545.1_ASM1629254v1_genomic.fna/tc_result.tsv
[2023-06-30 14:48:48,057] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:48:48,057] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:48:48,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6121b8ab-af60-4648-904d-31d3cc13597f/dqc_reference/checkm_data
[2023-06-30 14:48:48,058] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:48:48,090] [INFO] Task started: CheckM
[2023-06-30 14:48:48,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016292545.1_ASM1629254v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016292545.1_ASM1629254v1_genomic.fna/checkm_input GCA_016292545.1_ASM1629254v1_genomic.fna/checkm_result
[2023-06-30 14:49:38,407] [INFO] Task succeeded: CheckM
[2023-06-30 14:49:38,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 14:49:38,429] [INFO] ===== Completeness check finished =====
[2023-06-30 14:49:38,429] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:49:38,430] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016292545.1_ASM1629254v1_genomic.fna/markers.fasta)
[2023-06-30 14:49:38,430] [INFO] Task started: Blastn
[2023-06-30 14:49:38,430] [INFO] Running command: blastn -query GCA_016292545.1_ASM1629254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6121b8ab-af60-4648-904d-31d3cc13597f/dqc_reference/reference_markers_gtdb.fasta -out GCA_016292545.1_ASM1629254v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:49:39,706] [INFO] Task succeeded: Blastn
[2023-06-30 14:49:39,712] [INFO] Selected 21 target genomes.
[2023-06-30 14:49:39,712] [INFO] Target genome list was writen to GCA_016292545.1_ASM1629254v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:49:39,723] [INFO] Task started: fastANI
[2023-06-30 14:49:39,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgf972c46c-7443-4370-bfcb-7b9a96b64e8d/GCA_016292545.1_ASM1629254v1_genomic.fna.gz --refList GCA_016292545.1_ASM1629254v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016292545.1_ASM1629254v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:49:49,944] [INFO] Task succeeded: fastANI
[2023-06-30 14:49:49,965] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:49:49,966] [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_016292545.1	s__UBA4372 sp016292545	100.0	739	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900320435.1	s__UBA4372 sp900320435	77.758	93	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.93	95.36	0.84	0.75	10	-
GCA_002394305.1	s__UBA4372 sp002394305	77.6818	146	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.13	97.13	0.80	0.80	2	-
GCA_017379075.1	s__UBA4372 sp017379075	77.6632	180	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	95.81	95.71	0.83	0.83	3	-
GCA_017559845.1	s__UBA4372 sp017559845	77.5836	177	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622815.1	s__UBA4372 sp017622815	77.5128	119	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.97	96.79	0.85	0.83	4	-
GCA_002395775.1	s__UBA4372 sp002395775	77.4273	126	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.87	96.87	0.81	0.81	2	-
GCA_900543815.1	s__UBA4372 sp900543815	77.3942	188	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.82	97.58	0.92	0.88	4	-
GCA_017483665.1	s__UBA4372 sp017483665	77.3329	170	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935785.1	s__UBA4372 sp017935785	77.3129	180	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.67	97.67	0.84	0.84	2	-
GCA_017453445.1	s__UBA4372 sp017453445	77.1929	117	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.06	98.06	0.83	0.83	2	-
GCA_902787575.1	s__UBA4372 sp900320715	77.1076	126	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.55	98.27	0.96	0.94	8	-
GCA_902783655.1	s__UBA4372 sp902783655	77.0718	101	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776455.1	s__UBA4372 sp902776455	76.929	133	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.21	96.34	0.88	0.83	6	-
GCA_900548345.1	s__Paraprevotella sp900548345	76.8245	55	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	100.00	100.00	0.98	0.98	2	-
GCA_017455585.1	s__UBA4372 sp017455585	76.735	97	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017464815.1	s__Phocaeicola_A sp017464815	76.4445	87	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116805.1	s__Bacteroides merdavium	76.2093	51	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557285.1	s__Prevotella sp004557285	76.0871	57	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.35	98.35	0.77	0.77	2	-
GCA_017509155.1	s__Prevotella sp017509155	76.0469	70	744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:49:49,968] [INFO] GTDB search result was written to GCA_016292545.1_ASM1629254v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:49:49,968] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:49:49,972] [INFO] DFAST_QC result json was written to GCA_016292545.1_ASM1629254v1_genomic.fna/dqc_result.json
[2023-06-30 14:49:49,973] [INFO] DFAST_QC completed!
[2023-06-30 14:49:49,973] [INFO] Total running time: 0h1m38s