[2023-06-05 01:53:56,057] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:53:56,060] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:53:56,060] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4c01781-88f3-494d-b9b4-6a34ebe5d410/dqc_reference
[2023-06-05 01:53:58,251] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:53:58,252] [INFO] Task started: Prodigal
[2023-06-05 01:53:58,252] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f9510d6-b010-4aa9-8282-af84d3e8d1fa/GCA_934865005.1_MTG234_bin.49.fa_genomic.fna.gz | prodigal -d GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/cds.fna -a GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:54:03,572] [INFO] Task succeeded: Prodigal
[2023-06-05 01:54:03,572] [INFO] Task started: HMMsearch
[2023-06-05 01:54:03,573] [INFO] Running command: hmmsearch --tblout GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4c01781-88f3-494d-b9b4-6a34ebe5d410/dqc_reference/reference_markers.hmm GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:54:03,803] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:54:03,804] [INFO] Found 6/6 markers.
[2023-06-05 01:54:03,823] [INFO] Query marker FASTA was written to GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/markers.fasta
[2023-06-05 01:54:03,823] [INFO] Task started: Blastn
[2023-06-05 01:54:03,824] [INFO] Running command: blastn -query GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4c01781-88f3-494d-b9b4-6a34ebe5d410/dqc_reference/reference_markers.fasta -out GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:54:04,523] [INFO] Task succeeded: Blastn
[2023-06-05 01:54:04,526] [INFO] Selected 16 target genomes.
[2023-06-05 01:54:04,527] [INFO] Target genome list was writen to GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/target_genomes.txt
[2023-06-05 01:54:04,531] [INFO] Task started: fastANI
[2023-06-05 01:54:04,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f9510d6-b010-4aa9-8282-af84d3e8d1fa/GCA_934865005.1_MTG234_bin.49.fa_genomic.fna.gz --refList GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/target_genomes.txt --output GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:54:11,263] [INFO] Task succeeded: fastANI
[2023-06-05 01:54:11,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4c01781-88f3-494d-b9b4-6a34ebe5d410/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:54:11,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4c01781-88f3-494d-b9b4-6a34ebe5d410/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:54:11,285] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:54:11,285] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 01:54:11,286] [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
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	94.9744	504	547	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	94.959	502	547	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	94.9496	500	547	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.0987	198	547	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.8356	220	547	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.7947	220	547	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.644	194	547	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.4239	205	547	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.3498	193	547	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.1519	199	547	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	79.0146	140	547	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.8601	174	547	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 01:54:11,288] [INFO] DFAST Taxonomy check result was written to GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/tc_result.tsv
[2023-06-05 01:54:11,288] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:54:11,289] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:54:11,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4c01781-88f3-494d-b9b4-6a34ebe5d410/dqc_reference/checkm_data
[2023-06-05 01:54:11,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:54:11,315] [INFO] Task started: CheckM
[2023-06-05 01:54:11,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/checkm_input GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/checkm_result
[2023-06-05 01:54:33,244] [INFO] Task succeeded: CheckM
[2023-06-05 01:54:33,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:54:33,265] [INFO] ===== Completeness check finished =====
[2023-06-05 01:54:33,266] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:54:33,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/markers.fasta)
[2023-06-05 01:54:33,266] [INFO] Task started: Blastn
[2023-06-05 01:54:33,267] [INFO] Running command: blastn -query GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4c01781-88f3-494d-b9b4-6a34ebe5d410/dqc_reference/reference_markers_gtdb.fasta -out GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:54:34,569] [INFO] Task succeeded: Blastn
[2023-06-05 01:54:34,574] [INFO] Selected 33 target genomes.
[2023-06-05 01:54:34,574] [INFO] Target genome list was writen to GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:54:34,597] [INFO] Task started: fastANI
[2023-06-05 01:54:34,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f9510d6-b010-4aa9-8282-af84d3e8d1fa/GCA_934865005.1_MTG234_bin.49.fa_genomic.fna.gz --refList GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:54:47,683] [INFO] Task succeeded: fastANI
[2023-06-05 01:54:47,715] [INFO] Found 33 fastANI hits (6 hits with ANI > circumscription radius)
[2023-06-05 01:54:47,715] [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_019041915.1	s__Collinsella sp019041915	95.328	494	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.145	96.63	95.48	0.93	0.87	6	inconclusive
GCA_900541125.1	s__Collinsella sp900541125	95.3145	489	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2242	95.44	95.26	0.87	0.84	10	inconclusive
GCF_001405375.1	s__Collinsella aerofaciens_F	95.2558	496	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2147	95.33	95.22	0.89	0.87	8	inconclusive
GCF_015558785.1	s__Collinsella aerofaciens_P	95.1996	492	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1792	95.28	95.25	0.89	0.89	3	inconclusive
GCA_900544865.1	s__Collinsella sp900544865	95.1613	486	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_018381235.1	s__Collinsella sp018381235	95.1234	496	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0673	N/A	N/A	N/A	N/A	1	inconclusive
GCA_900752215.1	s__Collinsella sp900752215	95.0385	451	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0875	99.95	99.95	0.94	0.94	2	-
GCF_000763055.1	s__Collinsella sp000763055	94.9228	503	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902363125.1	s__Collinsella sp902363125	94.8922	486	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.02	96.02	0.87	0.87	2	-
GCA_900541135.1	s__Collinsella sp900541135	94.8699	482	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008668235.1	s__Collinsella aerofaciens_K	94.8519	452	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0357	97.54	95.17	0.89	0.81	5	-
GCA_900545505.1	s__Collinsella sp900545505	94.8352	325	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0349	N/A	N/A	N/A	N/A	1	-
GCA_900542905.1	s__Collinsella sp900542905	94.8259	479	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900752545.1	s__Collinsella sp900752545	94.7932	463	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.97	99.97	0.93	0.93	2	-
GCA_905213725.1	s__Collinsella aerofaciens_R	94.7853	419	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0706	99.79	99.79	0.97	0.97	2	-
GCF_015560765.1	s__Collinsella aerofaciens_M	94.7703	488	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1158	96.04	95.15	0.86	0.78	15	-
GCA_900551305.1	s__Collinsella sp900551305	94.729	328	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0792	96.10	95.39	0.89	0.68	9	-
GCA_900543025.1	s__Collinsella sp900543025	94.7029	463	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552385.1	s__Collinsella sp900552385	94.6686	381	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1029	95.27	95.27	0.73	0.73	2	-
GCA_900541795.1	s__Collinsella sp900541795	94.6619	488	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0323	N/A	N/A	N/A	N/A	1	-
GCA_900543605.1	s__Collinsella sp900543605	94.5655	448	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542305.1	s__Collinsella sp900542305	94.5308	467	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540895.1	s__Collinsella sp900540895	94.4615	486	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.25	95.25	0.87	0.87	2	-
GCA_900540905.1	s__Collinsella sp900540905	94.3935	473	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.97	0.97	2	-
GCA_018378775.1	s__Collinsella sp018378775	94.3174	451	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.51	95.51	0.75	0.75	2	-
GCA_900552755.1	s__Collinsella sp900552755	94.2478	384	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547285.1	s__Collinsella sp900547285	94.1942	409	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541645.1	s__Collinsella sp900541645	94.1012	476	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.32	95.32	0.85	0.85	2	-
GCA_900549535.1	s__Collinsella sp900549535	93.866	416	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761945.1	s__Collinsella sp900761945	93.5887	320	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556705.1	s__Collinsella sp900556705	93.2741	232	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900758475.1	s__Collinsella sp900758475	92.7684	460	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.39	95.09	0.82	0.79	4	-
GCA_900542825.1	s__Collinsella sp900542825	92.2678	451	547	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:54:47,717] [INFO] GTDB search result was written to GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 01:54:47,717] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:54:47,722] [INFO] DFAST_QC result json was written to GCA_934865005.1_MTG234_bin.49.fa_genomic.fna/dqc_result.json
[2023-06-05 01:54:47,722] [INFO] DFAST_QC completed!
[2023-06-05 01:54:47,722] [INFO] Total running time: 0h0m52s