[2023-06-19 10:56:15,343] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:56:15,345] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:56:15,345] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2a7e589-6a53-4441-8ba2-7c0fbe3010c2/dqc_reference
[2023-06-19 10:56:17,893] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:56:17,894] [INFO] Task started: Prodigal
[2023-06-19 10:56:17,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c7750b1-7757-41c3-bb79-2134ffa9c96a/GCA_018370025.1_ASM1837002v1_genomic.fna.gz | prodigal -d GCA_018370025.1_ASM1837002v1_genomic.fna/cds.fna -a GCA_018370025.1_ASM1837002v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:56:24,989] [INFO] Task succeeded: Prodigal
[2023-06-19 10:56:24,990] [INFO] Task started: HMMsearch
[2023-06-19 10:56:24,990] [INFO] Running command: hmmsearch --tblout GCA_018370025.1_ASM1837002v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2a7e589-6a53-4441-8ba2-7c0fbe3010c2/dqc_reference/reference_markers.hmm GCA_018370025.1_ASM1837002v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:56:25,226] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:56:25,228] [INFO] Found 6/6 markers.
[2023-06-19 10:56:25,286] [INFO] Query marker FASTA was written to GCA_018370025.1_ASM1837002v1_genomic.fna/markers.fasta
[2023-06-19 10:56:25,287] [INFO] Task started: Blastn
[2023-06-19 10:56:25,287] [INFO] Running command: blastn -query GCA_018370025.1_ASM1837002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2a7e589-6a53-4441-8ba2-7c0fbe3010c2/dqc_reference/reference_markers.fasta -out GCA_018370025.1_ASM1837002v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:56:25,928] [INFO] Task succeeded: Blastn
[2023-06-19 10:56:25,933] [INFO] Selected 19 target genomes.
[2023-06-19 10:56:25,933] [INFO] Target genome list was writen to GCA_018370025.1_ASM1837002v1_genomic.fna/target_genomes.txt
[2023-06-19 10:56:25,935] [INFO] Task started: fastANI
[2023-06-19 10:56:25,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c7750b1-7757-41c3-bb79-2134ffa9c96a/GCA_018370025.1_ASM1837002v1_genomic.fna.gz --refList GCA_018370025.1_ASM1837002v1_genomic.fna/target_genomes.txt --output GCA_018370025.1_ASM1837002v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:56:34,177] [INFO] Task succeeded: fastANI
[2023-06-19 10:56:34,178] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2a7e589-6a53-4441-8ba2-7c0fbe3010c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:56:34,178] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2a7e589-6a53-4441-8ba2-7c0fbe3010c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:56:34,197] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:56:34,197] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 10:56:34,198] [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=JCM 10188	GCA_010509075.1	74426	74426	type	True	94.75	589	698	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	94.7229	596	698	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	94.6569	598	698	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.4904	235	698	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.9038	266	698	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.8245	246	698	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.4979	245	698	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.4716	220	698	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	79.1919	183	698	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.0477	210	698	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 10:56:34,200] [INFO] DFAST Taxonomy check result was written to GCA_018370025.1_ASM1837002v1_genomic.fna/tc_result.tsv
[2023-06-19 10:56:34,201] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:56:34,201] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:56:34,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2a7e589-6a53-4441-8ba2-7c0fbe3010c2/dqc_reference/checkm_data
[2023-06-19 10:56:34,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:56:34,231] [INFO] Task started: CheckM
[2023-06-19 10:56:34,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018370025.1_ASM1837002v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018370025.1_ASM1837002v1_genomic.fna/checkm_input GCA_018370025.1_ASM1837002v1_genomic.fna/checkm_result
[2023-06-19 10:56:58,702] [INFO] Task succeeded: CheckM
[2023-06-19 10:56:58,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 10:56:58,722] [INFO] ===== Completeness check finished =====
[2023-06-19 10:56:58,723] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:56:58,723] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018370025.1_ASM1837002v1_genomic.fna/markers.fasta)
[2023-06-19 10:56:58,723] [INFO] Task started: Blastn
[2023-06-19 10:56:58,724] [INFO] Running command: blastn -query GCA_018370025.1_ASM1837002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2a7e589-6a53-4441-8ba2-7c0fbe3010c2/dqc_reference/reference_markers_gtdb.fasta -out GCA_018370025.1_ASM1837002v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:56:59,732] [INFO] Task succeeded: Blastn
[2023-06-19 10:56:59,737] [INFO] Selected 35 target genomes.
[2023-06-19 10:56:59,737] [INFO] Target genome list was writen to GCA_018370025.1_ASM1837002v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:56:59,747] [INFO] Task started: fastANI
[2023-06-19 10:56:59,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c7750b1-7757-41c3-bb79-2134ffa9c96a/GCA_018370025.1_ASM1837002v1_genomic.fna.gz --refList GCA_018370025.1_ASM1837002v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018370025.1_ASM1837002v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:57:14,740] [INFO] Task succeeded: fastANI
[2023-06-19 10:57:14,772] [INFO] Found 30 fastANI hits (4 hits with ANI > circumscription radius)
[2023-06-19 10:57:14,772] [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_015560765.1	s__Collinsella aerofaciens_M	95.7451	578	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1158	96.04	95.15	0.86	0.78	15	inconclusive
GCA_905215755.1	s__Collinsella sp905215755	95.192	539	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0833	N/A	N/A	N/A	N/A	1	inconclusive
GCA_008671135.1	s__Collinsella aerofaciens_J	95.1826	590	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2147	97.21	95.28	0.90	0.82	6	-
GCA_900541235.1	s__Collinsella sp900541235	95.0908	570	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.02	95.02	0.86	0.86	2	inconclusive
GCA_018380015.1	s__Collinsella sp018380015	95.0772	586	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1883	96.09	95.27	0.89	0.86	8	-
GCF_005844325.1	s__Collinsella aerofaciens_G	95.0408	582	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.009	96.00	95.07	0.90	0.86	20	inconclusive
GCA_018373675.1	s__Collinsella sp018373675	94.8772	572	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0912	N/A	N/A	N/A	N/A	1	-
GCA_900544465.1	s__Collinsella sp900544465	94.8548	428	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0579	100.00	100.00	0.98	0.98	2	-
GCA_018381235.1	s__Collinsella sp018381235	94.8416	595	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0673	N/A	N/A	N/A	N/A	1	-
GCA_900544865.1	s__Collinsella sp900544865	94.784	554	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542165.1	s__Collinsella sp900542165	94.7271	573	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0912	95.41	95.20	0.86	0.82	3	-
GCA_900752015.1	s__Collinsella sp900752015	94.7213	536	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1642	99.95	99.95	0.93	0.93	2	-
GCF_003438495.1	s__Collinsella sp003438495	94.6723	578	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900540895.1	s__Collinsella sp900540895	94.642	571	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.25	95.25	0.87	0.87	2	-
GCA_900554645.1	s__Collinsella sp900554645	94.6097	298	698	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	94.5993	504	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544845.1	s__Collinsella sp900544845	94.4889	533	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.87	98.87	0.87	0.87	2	-
GCA_900540995.1	s__Collinsella sp900540995	94.4707	552	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.96	99.96	0.96	0.96	2	-
GCA_900541885.1	s__Collinsella sp900541885	94.4507	575	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900548495.1	s__Collinsella sp900548495	94.388	519	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0367	N/A	N/A	N/A	N/A	1	-
GCA_900545615.1	s__Collinsella sp900545615	94.3767	524	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.94	99.94	0.92	0.92	2	-
GCA_900552295.1	s__Collinsella sp900552295	94.3246	375	698	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	94.2973	561	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905204635.1	s__Collinsella sp905204635	94.1908	373	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546455.1	s__Collinsella sp900546455	94.1666	512	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760245.1	s__Collinsella sp900760245	94.1403	468	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545055.1	s__Collinsella sp900545055	93.9477	467	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009876115.1	s__Collinsella aerofaciens_N	93.7907	572	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.84	99.84	0.98	0.98	2	-
GCA_900553165.1	s__Collinsella sp900553165	93.7729	323	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547125.1	s__Collinsella sp900547125	92.9689	476	698	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-06-19 10:57:14,774] [INFO] GTDB search result was written to GCA_018370025.1_ASM1837002v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:57:14,775] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:57:14,780] [INFO] DFAST_QC result json was written to GCA_018370025.1_ASM1837002v1_genomic.fna/dqc_result.json
[2023-06-19 10:57:14,780] [INFO] DFAST_QC completed!
[2023-06-19 10:57:14,780] [INFO] Total running time: 0h0m59s