[2023-06-29 13:43:21,615] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:43:21,624] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:43:21,625] [INFO] DQC Reference Directory: /var/lib/cwl/stg9577bea9-e74e-409c-89f7-95ff24790fea/dqc_reference
[2023-06-29 13:43:22,969] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:43:22,970] [INFO] Task started: Prodigal
[2023-06-29 13:43:22,970] [INFO] Running command: gunzip -c /var/lib/cwl/stgea77273e-9083-4a7f-b8d2-204b9e6e63ae/GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:43:30,055] [INFO] Task succeeded: Prodigal
[2023-06-29 13:43:30,056] [INFO] Task started: HMMsearch
[2023-06-29 13:43:30,056] [INFO] Running command: hmmsearch --tblout GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9577bea9-e74e-409c-89f7-95ff24790fea/dqc_reference/reference_markers.hmm GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:43:30,291] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:43:30,292] [INFO] Found 6/6 markers.
[2023-06-29 13:43:30,316] [INFO] Query marker FASTA was written to GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 13:43:30,316] [INFO] Task started: Blastn
[2023-06-29 13:43:30,316] [INFO] Running command: blastn -query GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9577bea9-e74e-409c-89f7-95ff24790fea/dqc_reference/reference_markers.fasta -out GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:43:31,090] [INFO] Task succeeded: Blastn
[2023-06-29 13:43:31,094] [INFO] Selected 15 target genomes.
[2023-06-29 13:43:31,094] [INFO] Target genome list was writen to GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 13:43:31,095] [INFO] Task started: fastANI
[2023-06-29 13:43:31,095] [INFO] Running command: fastANI --query /var/lib/cwl/stgea77273e-9083-4a7f-b8d2-204b9e6e63ae/GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:43:37,578] [INFO] Task succeeded: fastANI
[2023-06-29 13:43:37,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9577bea9-e74e-409c-89f7-95ff24790fea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:43:37,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9577bea9-e74e-409c-89f7-95ff24790fea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:43:37,590] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 13:43:37,590] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 13:43:37,590] [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 tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	97.0003	651	733	95	conclusive
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	81.6009	274	733	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	80.5454	285	733	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	80.5305	261	733	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.4441	284	733	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	79.5488	189	733	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	79.4916	243	733	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	79.4568	240	733	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.2041	243	733	95	below_threshold
Enorma phocaeensis	strain=Marseille-P3242	GCA_900186505.1	1871019	1871019	type	True	79.0449	200	733	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.9393	230	733	95	below_threshold
Collinsella vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	78.852	219	733	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	78.1723	151	733	95	below_threshold
Slackia faecicanis	strain=DSM 17537	GCA_003725295.1	255723	255723	type	True	77.6679	67	733	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:43:37,592] [INFO] DFAST Taxonomy check result was written to GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 13:43:37,593] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:43:37,593] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:43:37,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9577bea9-e74e-409c-89f7-95ff24790fea/dqc_reference/checkm_data
[2023-06-29 13:43:37,594] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:43:37,625] [INFO] Task started: CheckM
[2023-06-29 13:43:37,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 13:44:03,368] [INFO] Task succeeded: CheckM
[2023-06-29 13:44:03,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:44:03,392] [INFO] ===== Completeness check finished =====
[2023-06-29 13:44:03,392] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:44:03,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 13:44:03,393] [INFO] Task started: Blastn
[2023-06-29 13:44:03,393] [INFO] Running command: blastn -query GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9577bea9-e74e-409c-89f7-95ff24790fea/dqc_reference/reference_markers_gtdb.fasta -out GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:44:04,804] [INFO] Task succeeded: Blastn
[2023-06-29 13:44:04,808] [INFO] Selected 20 target genomes.
[2023-06-29 13:44:04,808] [INFO] Target genome list was writen to GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:44:04,821] [INFO] Task started: fastANI
[2023-06-29 13:44:04,821] [INFO] Running command: fastANI --query /var/lib/cwl/stgea77273e-9083-4a7f-b8d2-204b9e6e63ae/GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:44:12,869] [INFO] Task succeeded: fastANI
[2023-06-29 13:44:12,886] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:44:12,887] [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_000225705.1	s__Collinsella tanakaei	97.0003	651	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.30	95.17	0.91	0.86	6	conclusive
GCF_900119895.1	s__Collinsella phocaeensis	81.6017	274	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.56	95.56	0.87	0.87	2	-
GCF_008014645.1	s__Collinsella sp008014645	81.4395	328	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.90	97.84	0.90	0.89	3	-
GCA_900548365.1	s__Collinsella sp900548365	81.4112	330	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.98	0.98	2	-
GCF_003479805.1	s__Collinsella sp003479805	80.7541	258	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.77	98.33	0.94	0.90	6	-
GCA_900555585.1	s__Collinsella sp900555585	80.1976	126	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902362275.1	s__Collinsella sp902362275	80.1761	226	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.48	97.28	0.91	0.88	7	-
GCF_016900375.1	s__Collinsella sp002305035	80.0565	274	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.55	95.55	0.87	0.87	2	-
GCA_900544655.1	s__Parolsenella sp900544655	79.7663	97	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	99.93	99.93	0.89	0.89	2	-
GCF_900046475.1	s__Collinsella ihuae	79.5734	276	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.74	97.24	0.91	0.87	7	-
GCA_019117005.1	s__Collinsella stercoripullorum	79.5089	260	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.76	98.76	0.91	0.91	2	-
GCF_016901575.1	s__Limicola phocaeensis_A	79.4498	233	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Limicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002437815.1	s__Collinsella sp002437815	79.3243	199	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159765.1	s__Coprousia sp002159765	79.2704	231	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	97.90	97.74	0.89	0.88	3	-
GCA_900542555.1	s__Collinsella sp900542555	79.2461	217	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551185.1	s__Collinsella sp900551185	79.2191	170	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0395	95.41	95.41	0.89	0.89	2	-
GCF_902150035.1	s__Enorma burkinafasonensis	79.1807	244	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015062655.1	s__Collinsella sp015062655	79.147	227	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555745.1	s__Collinsella sp900555745	78.4424	118	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725295.1	s__Slackia_A faecicanis	77.7097	67	733	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:44:12,889] [INFO] GTDB search result was written to GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 13:44:12,889] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:44:12,894] [INFO] DFAST_QC result json was written to GCA_937981475.1_ERR3160563_bin.75_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 13:44:12,894] [INFO] DFAST_QC completed!
[2023-06-29 13:44:12,894] [INFO] Total running time: 0h0m51s