[2023-06-29 14:09:56,810] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:09:56,812] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:09:56,813] [INFO] DQC Reference Directory: /var/lib/cwl/stg21d3a02a-8848-40f8-a3ba-9081dcde52d8/dqc_reference
[2023-06-29 14:09:58,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:09:58,100] [INFO] Task started: Prodigal
[2023-06-29 14:09:58,100] [INFO] Running command: gunzip -c /var/lib/cwl/stg763d0925-97b9-4437-83da-648fdee2b9d0/GCA_910586995.1_MGBC153228_genomic.fna.gz | prodigal -d GCA_910586995.1_MGBC153228_genomic.fna/cds.fna -a GCA_910586995.1_MGBC153228_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:10:11,840] [INFO] Task succeeded: Prodigal
[2023-06-29 14:10:11,840] [INFO] Task started: HMMsearch
[2023-06-29 14:10:11,840] [INFO] Running command: hmmsearch --tblout GCA_910586995.1_MGBC153228_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21d3a02a-8848-40f8-a3ba-9081dcde52d8/dqc_reference/reference_markers.hmm GCA_910586995.1_MGBC153228_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:10:12,074] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:10:12,075] [INFO] Found 6/6 markers.
[2023-06-29 14:10:12,103] [INFO] Query marker FASTA was written to GCA_910586995.1_MGBC153228_genomic.fna/markers.fasta
[2023-06-29 14:10:12,103] [INFO] Task started: Blastn
[2023-06-29 14:10:12,103] [INFO] Running command: blastn -query GCA_910586995.1_MGBC153228_genomic.fna/markers.fasta -db /var/lib/cwl/stg21d3a02a-8848-40f8-a3ba-9081dcde52d8/dqc_reference/reference_markers.fasta -out GCA_910586995.1_MGBC153228_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:10:12,679] [INFO] Task succeeded: Blastn
[2023-06-29 14:10:12,684] [INFO] Selected 30 target genomes.
[2023-06-29 14:10:12,685] [INFO] Target genome list was writen to GCA_910586995.1_MGBC153228_genomic.fna/target_genomes.txt
[2023-06-29 14:10:12,690] [INFO] Task started: fastANI
[2023-06-29 14:10:12,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg763d0925-97b9-4437-83da-648fdee2b9d0/GCA_910586995.1_MGBC153228_genomic.fna.gz --refList GCA_910586995.1_MGBC153228_genomic.fna/target_genomes.txt --output GCA_910586995.1_MGBC153228_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:10:29,589] [INFO] Task succeeded: fastANI
[2023-06-29 14:10:29,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21d3a02a-8848-40f8-a3ba-9081dcde52d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:10:29,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21d3a02a-8848-40f8-a3ba-9081dcde52d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:10:29,602] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:10:29,602] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:10:29,603] [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
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	77.7538	60	812	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	77.6703	61	812	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	77.6583	60	812	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	77.197	68	812	95	below_threshold
Heminiphilus faecis	strain=AM35	GCA_008728965.1	2601703	2601703	type	True	77.0594	58	812	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	76.931	67	812	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	76.7884	74	812	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:10:29,605] [INFO] DFAST Taxonomy check result was written to GCA_910586995.1_MGBC153228_genomic.fna/tc_result.tsv
[2023-06-29 14:10:29,606] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:10:29,606] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:10:29,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21d3a02a-8848-40f8-a3ba-9081dcde52d8/dqc_reference/checkm_data
[2023-06-29 14:10:29,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:10:29,633] [INFO] Task started: CheckM
[2023-06-29 14:10:29,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910586995.1_MGBC153228_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910586995.1_MGBC153228_genomic.fna/checkm_input GCA_910586995.1_MGBC153228_genomic.fna/checkm_result
[2023-06-29 14:11:12,379] [INFO] Task succeeded: CheckM
[2023-06-29 14:11:12,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:11:12,410] [INFO] ===== Completeness check finished =====
[2023-06-29 14:11:12,411] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:11:12,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910586995.1_MGBC153228_genomic.fna/markers.fasta)
[2023-06-29 14:11:12,412] [INFO] Task started: Blastn
[2023-06-29 14:11:12,412] [INFO] Running command: blastn -query GCA_910586995.1_MGBC153228_genomic.fna/markers.fasta -db /var/lib/cwl/stg21d3a02a-8848-40f8-a3ba-9081dcde52d8/dqc_reference/reference_markers_gtdb.fasta -out GCA_910586995.1_MGBC153228_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:11:13,233] [INFO] Task succeeded: Blastn
[2023-06-29 14:11:13,238] [INFO] Selected 27 target genomes.
[2023-06-29 14:11:13,238] [INFO] Target genome list was writen to GCA_910586995.1_MGBC153228_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:11:13,247] [INFO] Task started: fastANI
[2023-06-29 14:11:13,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg763d0925-97b9-4437-83da-648fdee2b9d0/GCA_910586995.1_MGBC153228_genomic.fna.gz --refList GCA_910586995.1_MGBC153228_genomic.fna/target_genomes_gtdb.txt --output GCA_910586995.1_MGBC153228_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:11:24,665] [INFO] Task succeeded: fastANI
[2023-06-29 14:11:24,694] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:11:24,694] [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_910586995.1	s__CAG-873 sp910586995	100.0	809	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900548975.1	s__CAG-873 sp900548975	77.9607	59	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.98	99.96	0.94	0.89	3	-
GCA_910577255.1	s__Duncaniella sp910577255	77.7464	74	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002201515.1	s__Muribaculum intestinale	77.6354	59	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.09	97.90	0.92	0.80	20	-
GCA_900544535.1	s__Duncaniella sp900544535	77.3863	68	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910584825.1	s__Duncaniella sp910584825	77.2774	69	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014802345.1	s__Duncaniella sp014802345	77.2454	70	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.04	97.99	0.90	0.88	3	-
GCA_900762315.1	s__Duncaniella sp900762315	77.0548	57	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576785.1	s__Duncaniella sp910576785	77.0226	81	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431215.1	s__CAG-1031 sp000431215	76.9828	51	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-1031	95.0	98.67	97.81	0.89	0.82	6	-
GCA_910579995.1	s__CAG-873 sp009775135	76.9778	73	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.86	99.86	0.96	0.96	2	-
GCA_910577315.1	s__CAG-873 sp910577315	76.9594	78	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.79	97.79	0.88	0.88	2	-
GCF_004803695.1	s__Muribaculum gordoncarteri	76.9264	66	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	96.82	95.63	0.92	0.83	15	-
GCA_009775535.1	s__CAG-873 sp009775535	76.8798	78	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.05	98.75	0.86	0.77	3	-
GCA_009775225.1	s__CAG-873 sp009775225	76.852	70	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	98.13	98.13	0.88	0.86	3	-
GCA_910587545.1	s__CAG-873 sp910587545	76.8282	57	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540205.1	s__UBA7173 sp900540205	76.6939	69	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	96.71	95.96	0.83	0.74	4	-
GCA_900551515.1	s__Paramuribaculum sp900551515	76.6924	60	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577355.1	s__CAG-873 sp910577355	76.6896	70	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583865.1	s__Muribaculum sp910583865	76.6526	52	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004102805.1	s__UBA7173 sp004102805	76.6098	73	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	98.86	98.86	0.92	0.89	3	-
GCA_017624155.1	s__CAG-873 sp017624155	76.3898	52	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576935.1	s__CAG-873 sp910576935	76.3596	77	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:11:24,696] [INFO] GTDB search result was written to GCA_910586995.1_MGBC153228_genomic.fna/result_gtdb.tsv
[2023-06-29 14:11:24,697] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:11:24,709] [INFO] DFAST_QC result json was written to GCA_910586995.1_MGBC153228_genomic.fna/dqc_result.json
[2023-06-29 14:11:24,709] [INFO] DFAST_QC completed!
[2023-06-29 14:11:24,710] [INFO] Total running time: 0h1m28s