[2023-06-05 19:01:45,845] [INFO] DFAST_QC pipeline started.
[2023-06-05 19:01:45,867] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 19:01:45,867] [INFO] DQC Reference Directory: /var/lib/cwl/stg313136c8-c1fb-4a46-a125-b74edec3444b/dqc_reference
[2023-06-05 19:01:49,119] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 19:01:49,120] [INFO] Task started: Prodigal
[2023-06-05 19:01:49,120] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0e3c856-23aa-4025-8e53-618609bab71c/GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna.gz | prodigal -d GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/cds.fna -a GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 19:02:01,579] [INFO] Task succeeded: Prodigal
[2023-06-05 19:02:01,579] [INFO] Task started: HMMsearch
[2023-06-05 19:02:01,579] [INFO] Running command: hmmsearch --tblout GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg313136c8-c1fb-4a46-a125-b74edec3444b/dqc_reference/reference_markers.hmm GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/protein.faa > /dev/null
[2023-06-05 19:02:01,809] [INFO] Task succeeded: HMMsearch
[2023-06-05 19:02:01,811] [INFO] Found 6/6 markers.
[2023-06-05 19:02:01,851] [INFO] Query marker FASTA was written to GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/markers.fasta
[2023-06-05 19:02:01,852] [INFO] Task started: Blastn
[2023-06-05 19:02:01,852] [INFO] Running command: blastn -query GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/markers.fasta -db /var/lib/cwl/stg313136c8-c1fb-4a46-a125-b74edec3444b/dqc_reference/reference_markers.fasta -out GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:02:02,512] [INFO] Task succeeded: Blastn
[2023-06-05 19:02:02,516] [INFO] Selected 27 target genomes.
[2023-06-05 19:02:02,517] [INFO] Target genome list was writen to GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/target_genomes.txt
[2023-06-05 19:02:02,548] [INFO] Task started: fastANI
[2023-06-05 19:02:02,548] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0e3c856-23aa-4025-8e53-618609bab71c/GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna.gz --refList GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/target_genomes.txt --output GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 19:02:16,113] [INFO] Task succeeded: fastANI
[2023-06-05 19:02:16,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg313136c8-c1fb-4a46-a125-b74edec3444b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 19:02:16,115] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg313136c8-c1fb-4a46-a125-b74edec3444b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 19:02:16,129] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 19:02:16,129] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 19:02:16,129] [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	77.6895	123	623	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.2677	94	623	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.1013	138	623	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	77.0818	137	623	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	77.0756	137	623	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.9087	136	623	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.9081	105	623	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.8957	96	623	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.8392	103	623	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.6726	64	623	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.6253	118	623	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.5953	80	623	95	below_threshold
Prevotella multisaccharivorax	strain=JCM 12954	GCA_019973315.1	310514	310514	type	True	76.5123	67	623	95	below_threshold
Prevotella multisaccharivorax	strain=DSM 17128	GCA_000218235.1	310514	310514	type	True	76.4034	65	623	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 19:02:16,132] [INFO] DFAST Taxonomy check result was written to GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/tc_result.tsv
[2023-06-05 19:02:16,132] [INFO] ===== Taxonomy check completed =====
[2023-06-05 19:02:16,132] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 19:02:16,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg313136c8-c1fb-4a46-a125-b74edec3444b/dqc_reference/checkm_data
[2023-06-05 19:02:16,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 19:02:16,162] [INFO] Task started: CheckM
[2023-06-05 19:02:16,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/checkm_input GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/checkm_result
[2023-06-05 19:02:55,510] [INFO] Task succeeded: CheckM
[2023-06-05 19:02:55,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 19:02:55,531] [INFO] ===== Completeness check finished =====
[2023-06-05 19:02:55,531] [INFO] ===== Start GTDB Search =====
[2023-06-05 19:02:55,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/markers.fasta)
[2023-06-05 19:02:55,532] [INFO] Task started: Blastn
[2023-06-05 19:02:55,532] [INFO] Running command: blastn -query GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/markers.fasta -db /var/lib/cwl/stg313136c8-c1fb-4a46-a125-b74edec3444b/dqc_reference/reference_markers_gtdb.fasta -out GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:02:56,539] [INFO] Task succeeded: Blastn
[2023-06-05 19:02:56,545] [INFO] Selected 32 target genomes.
[2023-06-05 19:02:56,545] [INFO] Target genome list was writen to GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 19:02:56,565] [INFO] Task started: fastANI
[2023-06-05 19:02:56,566] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0e3c856-23aa-4025-8e53-618609bab71c/GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna.gz --refList GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/target_genomes_gtdb.txt --output GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 19:03:12,613] [INFO] Task succeeded: fastANI
[2023-06-05 19:03:12,635] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 19:03:12,635] [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_900318625.1	s__Prevotella sp900318625	98.1611	535	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.97	97.03	0.86	0.78	43	conclusive
GCA_902781315.1	s__Prevotella sp902781315	77.9681	177	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.55	96.55	0.79	0.79	2	-
GCA_002353555.1	s__Prevotella sp002353555	77.8878	159	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.57	0.79	0.77	3	-
GCA_902771785.1	s__Prevotella sp902771785	77.8128	158	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.01	98.01	0.87	0.87	2	-
GCA_902776685.1	s__Prevotella sp902776685	77.8089	157	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775475.1	s__Prevotella sp902775475	77.7456	185	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.69	98.51	0.89	0.87	7	-
GCA_900316285.1	s__Prevotella sp900316285	77.6484	149	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.02	95.37	0.87	0.79	21	-
GCA_900316295.1	s__Prevotella sp900316295	77.5928	115	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.23	97.08	0.85	0.70	10	-
GCA_905233825.1	s__Prevotella sp905233825	77.5823	101	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019052365.1	s__Prevotella sp000434975	77.4997	133	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCA_900320585.1	s__Prevotella sp900320585	77.3767	150	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.77	98.44	0.87	0.81	6	-
GCA_017442765.1	s__Prevotella sp017442765	77.3755	111	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317305.1	s__Prevotella sp900317305	77.3576	148	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	97.82	0.87	0.83	11	-
GCA_900554695.1	s__Prevotella sp900554695	77.2435	89	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.93	97.88	0.84	0.83	3	-
GCF_002251435.1	s__Prevotella sp002251435	77.2239	74	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902760315.1	s__Prevotella sp902760315	77.1924	116	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002392835.1	s__Prevotella sp002392835	77.1647	125	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.57	97.57	0.74	0.74	2	-
GCA_905233425.1	s__Prevotella sp905233425	77.15	167	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767045.1	s__Prevotella sp902767045	77.1439	145	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.95	96.95	0.81	0.81	2	-
GCA_902792685.1	s__Prevotella sp902792685	77.1088	103	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.79	96.68	0.73	0.71	4	-
GCF_000184945.1	s__Prevotella buccae	77.0837	139	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCA_900544495.1	s__Prevotella sp900544495	76.9812	106	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_017615355.1	s__Prevotella sp017615355	76.9681	112	623	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	76.9213	131	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.53	95.99	0.92	0.86	5	-
GCA_905373605.1	s__Prevotella sp905373605	76.8633	59	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900199655.1	s__Prevotella sp900199655	76.8461	126	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.91	99.91	0.98	0.98	2	-
GCF_000426585.1	s__Prevotella baroniae	76.8392	103	623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.79	98.01	0.95	0.92	4	-
--------------------------------------------------------------------------------
[2023-06-05 19:03:12,637] [INFO] GTDB search result was written to GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/result_gtdb.tsv
[2023-06-05 19:03:12,638] [INFO] ===== GTDB Search completed =====
[2023-06-05 19:03:12,643] [INFO] DFAST_QC result json was written to GCA_902770895.1_Rumen_uncultured_genome_RUG11617_genomic.fna/dqc_result.json
[2023-06-05 19:03:12,643] [INFO] DFAST_QC completed!
[2023-06-05 19:03:12,643] [INFO] Total running time: 0h1m27s