[2023-06-28 18:16:50,034] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:16:50,036] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:16:50,036] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b0775e2-d259-40ed-91c6-2404498922ee/dqc_reference
[2023-06-28 18:16:51,326] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:16:51,327] [INFO] Task started: Prodigal
[2023-06-28 18:16:51,327] [INFO] Running command: gunzip -c /var/lib/cwl/stg79e44e3d-54e3-4848-8c9d-ed62ea8c6e81/GCA_944322175.1_BRZ_RS_bin111_genomic.fna.gz | prodigal -d GCA_944322175.1_BRZ_RS_bin111_genomic.fna/cds.fna -a GCA_944322175.1_BRZ_RS_bin111_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:16:56,986] [INFO] Task succeeded: Prodigal
[2023-06-28 18:16:56,986] [INFO] Task started: HMMsearch
[2023-06-28 18:16:56,986] [INFO] Running command: hmmsearch --tblout GCA_944322175.1_BRZ_RS_bin111_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b0775e2-d259-40ed-91c6-2404498922ee/dqc_reference/reference_markers.hmm GCA_944322175.1_BRZ_RS_bin111_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:16:57,222] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:16:57,224] [INFO] Found 6/6 markers.
[2023-06-28 18:16:57,244] [INFO] Query marker FASTA was written to GCA_944322175.1_BRZ_RS_bin111_genomic.fna/markers.fasta
[2023-06-28 18:16:57,248] [INFO] Task started: Blastn
[2023-06-28 18:16:57,248] [INFO] Running command: blastn -query GCA_944322175.1_BRZ_RS_bin111_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b0775e2-d259-40ed-91c6-2404498922ee/dqc_reference/reference_markers.fasta -out GCA_944322175.1_BRZ_RS_bin111_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:16:57,915] [INFO] Task succeeded: Blastn
[2023-06-28 18:16:57,919] [INFO] Selected 21 target genomes.
[2023-06-28 18:16:57,920] [INFO] Target genome list was writen to GCA_944322175.1_BRZ_RS_bin111_genomic.fna/target_genomes.txt
[2023-06-28 18:16:57,922] [INFO] Task started: fastANI
[2023-06-28 18:16:57,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg79e44e3d-54e3-4848-8c9d-ed62ea8c6e81/GCA_944322175.1_BRZ_RS_bin111_genomic.fna.gz --refList GCA_944322175.1_BRZ_RS_bin111_genomic.fna/target_genomes.txt --output GCA_944322175.1_BRZ_RS_bin111_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:17:06,176] [INFO] Task succeeded: fastANI
[2023-06-28 18:17:06,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b0775e2-d259-40ed-91c6-2404498922ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:17:06,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b0775e2-d259-40ed-91c6-2404498922ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:17:06,192] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:17:06,192] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:17:06,193] [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
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	80.2305	233	617	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.7915	281	617	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.5042	215	617	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	79.4339	221	617	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.061	222	617	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	78.987	219	617	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	78.9731	202	617	95	below_threshold
Enorma massiliensis		GCA_000311845.1	1472761	1472761	type	True	78.9725	215	617	95	below_threshold
Enorma shizhengliae	strain=HF-1365	GCA_009676995.1	2606615	2606615	type	True	78.9072	220	617	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	78.8831	174	617	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	78.6007	170	617	95	below_threshold
Collinsella vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	78.5846	178	617	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	78.5454	172	617	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	78.4319	175	617	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	78.3865	169	617	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	78.3259	180	617	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	78.2645	170	617	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	78.2179	166	617	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	78.101	171	617	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	77.3315	108	617	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	77.3158	107	617	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:17:06,195] [INFO] DFAST Taxonomy check result was written to GCA_944322175.1_BRZ_RS_bin111_genomic.fna/tc_result.tsv
[2023-06-28 18:17:06,195] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:17:06,195] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:17:06,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b0775e2-d259-40ed-91c6-2404498922ee/dqc_reference/checkm_data
[2023-06-28 18:17:06,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:17:06,220] [INFO] Task started: CheckM
[2023-06-28 18:17:06,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944322175.1_BRZ_RS_bin111_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944322175.1_BRZ_RS_bin111_genomic.fna/checkm_input GCA_944322175.1_BRZ_RS_bin111_genomic.fna/checkm_result
[2023-06-28 18:17:28,704] [INFO] Task succeeded: CheckM
[2023-06-28 18:17:28,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 18:17:28,731] [INFO] ===== Completeness check finished =====
[2023-06-28 18:17:28,731] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:17:28,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944322175.1_BRZ_RS_bin111_genomic.fna/markers.fasta)
[2023-06-28 18:17:28,732] [INFO] Task started: Blastn
[2023-06-28 18:17:28,732] [INFO] Running command: blastn -query GCA_944322175.1_BRZ_RS_bin111_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b0775e2-d259-40ed-91c6-2404498922ee/dqc_reference/reference_markers_gtdb.fasta -out GCA_944322175.1_BRZ_RS_bin111_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:17:29,834] [INFO] Task succeeded: Blastn
[2023-06-28 18:17:29,839] [INFO] Selected 26 target genomes.
[2023-06-28 18:17:29,839] [INFO] Target genome list was writen to GCA_944322175.1_BRZ_RS_bin111_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:17:29,882] [INFO] Task started: fastANI
[2023-06-28 18:17:29,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg79e44e3d-54e3-4848-8c9d-ed62ea8c6e81/GCA_944322175.1_BRZ_RS_bin111_genomic.fna.gz --refList GCA_944322175.1_BRZ_RS_bin111_genomic.fna/target_genomes_gtdb.txt --output GCA_944322175.1_BRZ_RS_bin111_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:17:40,427] [INFO] Task succeeded: fastANI
[2023-06-28 18:17:40,447] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:17:40,448] [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_002159765.1	s__Coprousia sp002159765	80.2892	264	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	97.90	97.74	0.89	0.88	3	-
GCA_000333815.1	s__Enorma sp000333815	80.2024	234	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	98.98	97.01	0.95	0.87	4	-
GCF_002161805.1	s__Coprousia sp002161805	80.0048	256	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016902615.1	s__Collinsella tanakaei_A	79.97	271	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.95	98.95	0.92	0.92	2	-
GCF_900046475.1	s__Collinsella ihuae	79.9623	264	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.74	97.24	0.91	0.87	7	-
GCF_016900375.1	s__Collinsella sp002305035	79.9405	297	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.55	95.55	0.87	0.87	2	-
GCA_018715125.1	s__Coprousia avicola	79.8535	270	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902150035.1	s__Enorma burkinafasonensis	79.7907	281	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159495.1	s__Thermophilibacter sp002159495	79.5714	231	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899935.1	s__Thermophilibacter uli_B	79.468	216	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160065.1	s__Limicola sp002160065	79.3722	248	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Limicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901575.1	s__Limicola phocaeensis_A	79.3518	251	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Limicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159625.1	s__Thermophilibacter avicola	79.2243	238	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.98	97.98	0.90	0.90	2	-
GCA_019116265.1	s__Thermophilibacter stercoravium	79.1342	183	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015062655.1	s__Collinsella sp015062655	79.1308	201	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156215.1	s__Collinsella stercoris	79.0401	223	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.61	95.23	0.87	0.81	5	-
GCF_900119895.1	s__Collinsella phocaeensis	78.9954	201	617	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	78.882	186	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.90	97.84	0.90	0.89	3	-
GCA_002437815.1	s__Collinsella sp002437815	78.5452	181	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780325.1	s__Parafannyhessea sp902787335	78.422	142	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.70	97.32	0.78	0.75	9	-
GCF_000225705.1	s__Collinsella tanakaei	78.3472	179	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.30	95.17	0.91	0.86	6	-
GCA_905214525.1	s__Collinsella sp905214525	78.3297	187	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.3232	N/A	N/A	N/A	N/A	1	-
GCA_900545505.1	s__Collinsella sp900545505	78.2095	117	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0349	N/A	N/A	N/A	N/A	1	-
GCA_902795065.1	s__RUG721 sp900321745	78.1342	145	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG721	95.0	99.01	98.55	0.89	0.82	11	-
GCA_900552395.1	s__Collinsella sp900552395	78.0632	145	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.15	N/A	N/A	N/A	N/A	1	-
GCF_000143845.1	s__Olsenella uli	77.3158	107	617	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella	95.0	99.32	99.02	0.94	0.91	5	-
--------------------------------------------------------------------------------
[2023-06-28 18:17:40,450] [INFO] GTDB search result was written to GCA_944322175.1_BRZ_RS_bin111_genomic.fna/result_gtdb.tsv
[2023-06-28 18:17:40,450] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:17:40,455] [INFO] DFAST_QC result json was written to GCA_944322175.1_BRZ_RS_bin111_genomic.fna/dqc_result.json
[2023-06-28 18:17:40,456] [INFO] DFAST_QC completed!
[2023-06-28 18:17:40,456] [INFO] Total running time: 0h0m50s