[2023-06-28 15:27:00,878] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:27:00,888] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:27:00,888] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c425f08-55f3-4231-a1a2-8a5a60221207/dqc_reference
[2023-06-28 15:27:01,987] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:27:01,988] [INFO] Task started: Prodigal
[2023-06-28 15:27:01,988] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf221ca2-c0a5-4485-8e16-6109546e93de/GCA_944320765.1_BRZ_CP_bin65_genomic.fna.gz | prodigal -d GCA_944320765.1_BRZ_CP_bin65_genomic.fna/cds.fna -a GCA_944320765.1_BRZ_CP_bin65_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:27:18,483] [INFO] Task succeeded: Prodigal
[2023-06-28 15:27:18,483] [INFO] Task started: HMMsearch
[2023-06-28 15:27:18,483] [INFO] Running command: hmmsearch --tblout GCA_944320765.1_BRZ_CP_bin65_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c425f08-55f3-4231-a1a2-8a5a60221207/dqc_reference/reference_markers.hmm GCA_944320765.1_BRZ_CP_bin65_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:27:18,666] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:27:18,667] [INFO] Found 6/6 markers.
[2023-06-28 15:27:18,693] [INFO] Query marker FASTA was written to GCA_944320765.1_BRZ_CP_bin65_genomic.fna/markers.fasta
[2023-06-28 15:27:18,693] [INFO] Task started: Blastn
[2023-06-28 15:27:18,693] [INFO] Running command: blastn -query GCA_944320765.1_BRZ_CP_bin65_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c425f08-55f3-4231-a1a2-8a5a60221207/dqc_reference/reference_markers.fasta -out GCA_944320765.1_BRZ_CP_bin65_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:27:19,255] [INFO] Task succeeded: Blastn
[2023-06-28 15:27:19,258] [INFO] Selected 19 target genomes.
[2023-06-28 15:27:19,258] [INFO] Target genome list was writen to GCA_944320765.1_BRZ_CP_bin65_genomic.fna/target_genomes.txt
[2023-06-28 15:27:19,259] [INFO] Task started: fastANI
[2023-06-28 15:27:19,259] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf221ca2-c0a5-4485-8e16-6109546e93de/GCA_944320765.1_BRZ_CP_bin65_genomic.fna.gz --refList GCA_944320765.1_BRZ_CP_bin65_genomic.fna/target_genomes.txt --output GCA_944320765.1_BRZ_CP_bin65_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:27:30,358] [INFO] Task succeeded: fastANI
[2023-06-28 15:27:30,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c425f08-55f3-4231-a1a2-8a5a60221207/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:27:30,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c425f08-55f3-4231-a1a2-8a5a60221207/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:27:30,368] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 15:27:30,368] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 15:27:30,368] [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
Paraprevotella clara	strain=YIT 11840	GCA_000233955.1	454154	454154	type	True	79.2067	434	953	95	below_threshold
Paraprevotella xylaniphila	strain=YIT 11841	GCA_000205165.1	454155	454155	type	True	79.0423	450	953	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	77.3527	117	953	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	77.2271	84	953	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	76.8789	75	953	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	76.7413	92	953	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	76.6952	95	953	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	76.6576	72	953	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.5996	70	953	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	76.5602	75	953	95	below_threshold
Bacteroides zoogleoformans	strain=ATCC 33285	GCA_007830715.1	28119	28119	type	True	76.5039	79	953	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	76.4687	67	953	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.4645	67	953	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	76.4627	66	953	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	75.9349	69	953	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 15:27:30,370] [INFO] DFAST Taxonomy check result was written to GCA_944320765.1_BRZ_CP_bin65_genomic.fna/tc_result.tsv
[2023-06-28 15:27:30,371] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:27:30,371] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:27:30,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c425f08-55f3-4231-a1a2-8a5a60221207/dqc_reference/checkm_data
[2023-06-28 15:27:30,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:27:30,401] [INFO] Task started: CheckM
[2023-06-28 15:27:30,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320765.1_BRZ_CP_bin65_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320765.1_BRZ_CP_bin65_genomic.fna/checkm_input GCA_944320765.1_BRZ_CP_bin65_genomic.fna/checkm_result
[2023-06-28 15:28:14,895] [INFO] Task succeeded: CheckM
[2023-06-28 15:28:14,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:28:14,911] [INFO] ===== Completeness check finished =====
[2023-06-28 15:28:14,911] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:28:14,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320765.1_BRZ_CP_bin65_genomic.fna/markers.fasta)
[2023-06-28 15:28:14,911] [INFO] Task started: Blastn
[2023-06-28 15:28:14,912] [INFO] Running command: blastn -query GCA_944320765.1_BRZ_CP_bin65_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c425f08-55f3-4231-a1a2-8a5a60221207/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320765.1_BRZ_CP_bin65_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:28:15,724] [INFO] Task succeeded: Blastn
[2023-06-28 15:28:15,727] [INFO] Selected 16 target genomes.
[2023-06-28 15:28:15,727] [INFO] Target genome list was writen to GCA_944320765.1_BRZ_CP_bin65_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:28:15,765] [INFO] Task started: fastANI
[2023-06-28 15:28:15,765] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf221ca2-c0a5-4485-8e16-6109546e93de/GCA_944320765.1_BRZ_CP_bin65_genomic.fna.gz --refList GCA_944320765.1_BRZ_CP_bin65_genomic.fna/target_genomes_gtdb.txt --output GCA_944320765.1_BRZ_CP_bin65_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:28:23,611] [INFO] Task succeeded: fastANI
[2023-06-28 15:28:23,621] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 15:28:23,622] [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
GCF_000233955.1	s__Paraprevotella clara	79.2059	434	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	97.73	97.27	0.87	0.80	9	-
GCF_000205165.1	s__Paraprevotella xylaniphila	79.0272	452	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	98.99	98.53	0.93	0.88	5	-
GCA_900548345.1	s__Paraprevotella sp900548345	78.1566	261	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	100.00	100.00	0.98	0.98	2	-
GCA_910586505.1	s__Paraprevotella sp910586505	77.9655	245	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760455.1	s__Paraprevotella sp900760455	77.5721	164	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	96.69	96.51	0.74	0.73	3	-
GCF_900291465.1	s__Phocaeicola_A sp900291465	77.5647	144	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola_A	95.0	97.97	97.87	0.87	0.85	4	-
GCA_017937925.1	s__Paraprevotella sp017937925	77.5364	61	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	98.10	97.94	0.89	0.89	3	-
GCA_019116285.1	s__Bacteroides merdigallinarum	77.349	141	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546665.1	s__Paraprevotella stercorigallinarum	77.3397	112	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	99.24	99.20	0.80	0.74	3	-
GCF_003477995.1	s__Paraprevotella sp003477995	77.1298	145	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	98.53	97.92	0.95	0.91	5	-
GCA_910584955.1	s__Paraprevotella sp910584955	76.9214	142	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320435.1	s__UBA4372 sp900320435	76.9113	103	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.93	95.36	0.84	0.75	10	-
GCA_018883665.1	s__Paraprevotella stercoravium	76.9108	83	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374585.1	s__Phocaeicola barnesiae	76.7072	92	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
GCF_900128495.1	s__Phocaeicola ilei	76.4504	55	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.42	98.42	0.92	0.92	2	-
GCA_905215575.1	s__Paraprevotella sp905215575	76.1911	66	953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 15:28:23,623] [INFO] GTDB search result was written to GCA_944320765.1_BRZ_CP_bin65_genomic.fna/result_gtdb.tsv
[2023-06-28 15:28:23,624] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:28:23,627] [INFO] DFAST_QC result json was written to GCA_944320765.1_BRZ_CP_bin65_genomic.fna/dqc_result.json
[2023-06-28 15:28:23,627] [INFO] DFAST_QC completed!
[2023-06-28 15:28:23,627] [INFO] Total running time: 0h1m23s