[2023-06-05 18:35:07,362] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:35:07,369] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:35:07,369] [INFO] DQC Reference Directory: /var/lib/cwl/stg43ade438-0a6b-4c69-b45a-ed55c10b7949/dqc_reference
[2023-06-05 18:35:09,229] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:35:09,230] [INFO] Task started: Prodigal
[2023-06-05 18:35:09,230] [INFO] Running command: gunzip -c /var/lib/cwl/stgc525ea01-ff38-46c4-acd5-d94d15bf1676/GCA_934630955.1_ERR7745438_bin.74_genomic.fna.gz | prodigal -d GCA_934630955.1_ERR7745438_bin.74_genomic.fna/cds.fna -a GCA_934630955.1_ERR7745438_bin.74_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:35:13,855] [INFO] Task succeeded: Prodigal
[2023-06-05 18:35:13,855] [INFO] Task started: HMMsearch
[2023-06-05 18:35:13,855] [INFO] Running command: hmmsearch --tblout GCA_934630955.1_ERR7745438_bin.74_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43ade438-0a6b-4c69-b45a-ed55c10b7949/dqc_reference/reference_markers.hmm GCA_934630955.1_ERR7745438_bin.74_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:35:14,021] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:35:14,023] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc525ea01-ff38-46c4-acd5-d94d15bf1676/GCA_934630955.1_ERR7745438_bin.74_genomic.fna.gz]
[2023-06-05 18:35:14,048] [INFO] Query marker FASTA was written to GCA_934630955.1_ERR7745438_bin.74_genomic.fna/markers.fasta
[2023-06-05 18:35:14,048] [INFO] Task started: Blastn
[2023-06-05 18:35:14,048] [INFO] Running command: blastn -query GCA_934630955.1_ERR7745438_bin.74_genomic.fna/markers.fasta -db /var/lib/cwl/stg43ade438-0a6b-4c69-b45a-ed55c10b7949/dqc_reference/reference_markers.fasta -out GCA_934630955.1_ERR7745438_bin.74_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:35:14,750] [INFO] Task succeeded: Blastn
[2023-06-05 18:35:14,759] [INFO] Selected 18 target genomes.
[2023-06-05 18:35:14,759] [INFO] Target genome list was writen to GCA_934630955.1_ERR7745438_bin.74_genomic.fna/target_genomes.txt
[2023-06-05 18:35:14,786] [INFO] Task started: fastANI
[2023-06-05 18:35:14,786] [INFO] Running command: fastANI --query /var/lib/cwl/stgc525ea01-ff38-46c4-acd5-d94d15bf1676/GCA_934630955.1_ERR7745438_bin.74_genomic.fna.gz --refList GCA_934630955.1_ERR7745438_bin.74_genomic.fna/target_genomes.txt --output GCA_934630955.1_ERR7745438_bin.74_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:35:23,128] [INFO] Task succeeded: fastANI
[2023-06-05 18:35:23,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43ade438-0a6b-4c69-b45a-ed55c10b7949/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:35:23,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43ade438-0a6b-4c69-b45a-ed55c10b7949/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:35:23,137] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:35:23,138] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:35:23,138] [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=ATCC 25986	GCA_000169035.1	74426	74426	type	True	92.2706	388	470	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	92.1247	406	470	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	92.0327	402	470	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	79.9583	164	470	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.5463	174	470	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.3997	153	470	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.3027	159	470	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.8899	137	470	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	78.5634	164	470	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:35:23,140] [INFO] DFAST Taxonomy check result was written to GCA_934630955.1_ERR7745438_bin.74_genomic.fna/tc_result.tsv
[2023-06-05 18:35:23,141] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:35:23,141] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:35:23,141] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43ade438-0a6b-4c69-b45a-ed55c10b7949/dqc_reference/checkm_data
[2023-06-05 18:35:23,142] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:35:23,162] [INFO] Task started: CheckM
[2023-06-05 18:35:23,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934630955.1_ERR7745438_bin.74_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934630955.1_ERR7745438_bin.74_genomic.fna/checkm_input GCA_934630955.1_ERR7745438_bin.74_genomic.fna/checkm_result
[2023-06-05 18:35:42,425] [INFO] Task succeeded: CheckM
[2023-06-05 18:35:42,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:35:42,446] [INFO] ===== Completeness check finished =====
[2023-06-05 18:35:42,447] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:35:42,447] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934630955.1_ERR7745438_bin.74_genomic.fna/markers.fasta)
[2023-06-05 18:35:42,447] [INFO] Task started: Blastn
[2023-06-05 18:35:42,447] [INFO] Running command: blastn -query GCA_934630955.1_ERR7745438_bin.74_genomic.fna/markers.fasta -db /var/lib/cwl/stg43ade438-0a6b-4c69-b45a-ed55c10b7949/dqc_reference/reference_markers_gtdb.fasta -out GCA_934630955.1_ERR7745438_bin.74_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:35:43,710] [INFO] Task succeeded: Blastn
[2023-06-05 18:35:43,715] [INFO] Selected 29 target genomes.
[2023-06-05 18:35:43,715] [INFO] Target genome list was writen to GCA_934630955.1_ERR7745438_bin.74_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:35:43,741] [INFO] Task started: fastANI
[2023-06-05 18:35:43,741] [INFO] Running command: fastANI --query /var/lib/cwl/stgc525ea01-ff38-46c4-acd5-d94d15bf1676/GCA_934630955.1_ERR7745438_bin.74_genomic.fna.gz --refList GCA_934630955.1_ERR7745438_bin.74_genomic.fna/target_genomes_gtdb.txt --output GCA_934630955.1_ERR7745438_bin.74_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:35:56,833] [INFO] Task succeeded: fastANI
[2023-06-05 18:35:56,852] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:35:56,853] [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_900755005.1	s__Collinsella sp900755005	92.6448	372	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.91	99.91	0.90	0.90	2	-
GCA_900547805.1	s__Collinsella sp900547805	92.6322	330	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003470665.1	s__Collinsella sp003470665	92.4223	389	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015552075.1	s__Collinsella aerofaciens_Y	92.3989	387	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540855.1	s__Collinsella sp900540855	92.3818	393	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.88	95.32	0.93	0.90	4	-
GCF_003462685.1	s__Collinsella sp003462685	92.3291	402	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.85	99.71	0.99	0.99	3	-
GCA_900542125.1	s__Collinsella sp900542125	92.2619	372	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541025.1	s__Collinsella sp900541025	92.1295	364	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542945.1	s__Collinsella sp900542945	92.0945	368	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1063	100.00	100.00	0.99	0.99	2	-
GCA_900541725.1	s__Collinsella sp900541725	92.0866	379	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900544065.1	s__Collinsella sp900544065	92.0402	349	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905209455.1	s__Collinsella sp905209455	92.0316	373	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1399	99.94	99.94	0.95	0.95	2	-
GCF_018785245.1	s__Collinsella aerofaciens_AD	91.956	369	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1928	N/A	N/A	N/A	N/A	1	-
GCA_900541715.1	s__Collinsella sp900541715	91.927	351	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0922	N/A	N/A	N/A	N/A	1	-
GCA_900551655.1	s__Collinsella sp900551655	91.8278	270	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548515.1	s__Collinsella sp900548515	91.826	350	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757385.1	s__Collinsella sp900757385	91.6918	298	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900767675.1	s__Collinsella sp900767675	91.6021	379	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549185.1	s__Collinsella sp900549185	91.3484	318	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544725.1	s__Collinsella sp900544725	91.1855	357	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551605.1	s__Collinsella sp900551605	91.1537	258	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.27	95.27	0.92	0.92	2	-
GCA_900541045.1	s__Collinsella sp900541045	91.1419	378	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761145.1	s__Collinsella sp900761145	91.0568	338	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554595.1	s__Collinsella sp900554595	90.9667	301	470	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.17	95.17	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-05 18:35:56,854] [INFO] GTDB search result was written to GCA_934630955.1_ERR7745438_bin.74_genomic.fna/result_gtdb.tsv
[2023-06-05 18:35:56,855] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:35:56,859] [INFO] DFAST_QC result json was written to GCA_934630955.1_ERR7745438_bin.74_genomic.fna/dqc_result.json
[2023-06-05 18:35:56,859] [INFO] DFAST_QC completed!
[2023-06-05 18:35:56,859] [INFO] Total running time: 0h0m49s