[2024-01-24 15:18:38,636] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:38,637] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:38,638] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2a207d9-d431-4f37-bd4d-22b1113e4f78/dqc_reference
[2024-01-24 15:18:39,839] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:39,840] [INFO] Task started: Prodigal
[2024-01-24 15:18:39,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg434057ce-cc5c-42dd-8833-ce5afd495635/GCF_900461335.1_50279_E02_genomic.fna.gz | prodigal -d GCF_900461335.1_50279_E02_genomic.fna/cds.fna -a GCF_900461335.1_50279_E02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:47,692] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:47,692] [INFO] Task started: HMMsearch
[2024-01-24 15:18:47,692] [INFO] Running command: hmmsearch --tblout GCF_900461335.1_50279_E02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2a207d9-d431-4f37-bd4d-22b1113e4f78/dqc_reference/reference_markers.hmm GCF_900461335.1_50279_E02_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:47,983] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:47,984] [INFO] Found 6/6 markers.
[2024-01-24 15:18:48,019] [INFO] Query marker FASTA was written to GCF_900461335.1_50279_E02_genomic.fna/markers.fasta
[2024-01-24 15:18:48,020] [INFO] Task started: Blastn
[2024-01-24 15:18:48,020] [INFO] Running command: blastn -query GCF_900461335.1_50279_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2a207d9-d431-4f37-bd4d-22b1113e4f78/dqc_reference/reference_markers.fasta -out GCF_900461335.1_50279_E02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:49,273] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:49,276] [INFO] Selected 15 target genomes.
[2024-01-24 15:18:49,276] [INFO] Target genome list was writen to GCF_900461335.1_50279_E02_genomic.fna/target_genomes.txt
[2024-01-24 15:18:49,291] [INFO] Task started: fastANI
[2024-01-24 15:18:49,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg434057ce-cc5c-42dd-8833-ce5afd495635/GCF_900461335.1_50279_E02_genomic.fna.gz --refList GCF_900461335.1_50279_E02_genomic.fna/target_genomes.txt --output GCF_900461335.1_50279_E02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:57,873] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:57,873] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2a207d9-d431-4f37-bd4d-22b1113e4f78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:57,873] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2a207d9-d431-4f37-bd4d-22b1113e4f78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:57,883] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:18:57,883] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:57,883] [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	100.0	815	819	95	conclusive
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	99.9941	811	819	95	conclusive
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	99.9781	793	819	95	conclusive
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.8198	248	819	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.3871	294	819	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	80.1592	291	819	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.971	250	819	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.7742	257	819	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.5103	249	819	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	79.4093	187	819	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.9996	219	819	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:57,890] [INFO] DFAST Taxonomy check result was written to GCF_900461335.1_50279_E02_genomic.fna/tc_result.tsv
[2024-01-24 15:18:57,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:57,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:57,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2a207d9-d431-4f37-bd4d-22b1113e4f78/dqc_reference/checkm_data
[2024-01-24 15:18:57,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:57,923] [INFO] Task started: CheckM
[2024-01-24 15:18:57,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900461335.1_50279_E02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900461335.1_50279_E02_genomic.fna/checkm_input GCF_900461335.1_50279_E02_genomic.fna/checkm_result
[2024-01-24 15:19:27,660] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:27,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:27,684] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:27,685] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:27,685] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900461335.1_50279_E02_genomic.fna/markers.fasta)
[2024-01-24 15:19:27,686] [INFO] Task started: Blastn
[2024-01-24 15:19:27,686] [INFO] Running command: blastn -query GCF_900461335.1_50279_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2a207d9-d431-4f37-bd4d-22b1113e4f78/dqc_reference/reference_markers_gtdb.fasta -out GCF_900461335.1_50279_E02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:29,167] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:29,170] [INFO] Selected 28 target genomes.
[2024-01-24 15:19:29,171] [INFO] Target genome list was writen to GCF_900461335.1_50279_E02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:29,191] [INFO] Task started: fastANI
[2024-01-24 15:19:29,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg434057ce-cc5c-42dd-8833-ce5afd495635/GCF_900461335.1_50279_E02_genomic.fna.gz --refList GCF_900461335.1_50279_E02_genomic.fna/target_genomes_gtdb.txt --output GCF_900461335.1_50279_E02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:43,094] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:43,119] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:43,120] [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_010509075.1	s__Collinsella aerofaciens	99.994	810	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.99	99.98	1.00	0.99	4	conclusive
GCA_900543515.1	s__Collinsella sp900543515	94.6542	572	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1148	100.00	100.00	0.98	0.98	2	-
GCA_900550825.1	s__Collinsella sp900550825	94.6298	477	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900541795.1	s__Collinsella sp900541795	94.6177	621	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0323	N/A	N/A	N/A	N/A	1	-
GCA_018381235.1	s__Collinsella sp018381235	94.5969	631	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0673	N/A	N/A	N/A	N/A	1	-
GCA_900544465.1	s__Collinsella sp900544465	94.5568	453	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0579	100.00	100.00	0.98	0.98	2	-
GCA_900541885.1	s__Collinsella sp900541885	94.5268	612	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900761085.1	s__Collinsella sp900761085	94.469	485	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545165.1	s__Collinsella sp900545165	94.4376	514	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761155.1	s__Collinsella sp900761155	94.4127	525	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759565.1	s__Collinsella sp900759565	94.4088	563	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.12	95.02	0.84	0.84	3	-
GCA_900539735.1	s__Collinsella sp900539735	94.3725	542	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541185.1	s__Collinsella sp900541185	94.3636	558	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.043	N/A	N/A	N/A	N/A	1	-
GCA_905199225.1	s__Collinsella sp900554665	94.3607	599	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900544845.1	s__Collinsella sp900544845	94.316	560	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.87	98.87	0.87	0.87	2	-
GCA_900757505.1	s__Collinsella sp900757505	94.1671	559	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014871545.1	s__Collinsella sp014871545	94.1222	391	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0116	N/A	N/A	N/A	N/A	1	-
GCA_900545605.1	s__Collinsella sp900545605	94.1035	571	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552755.1	s__Collinsella sp900552755	94.1027	454	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018380195.1	s__Collinsella sp018380195	94.0862	617	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.09	95.09	0.91	0.91	2	-
GCA_900552295.1	s__Collinsella sp900552295	94.0695	396	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905197385.1	s__Collinsella sp905197385	93.9307	378	819	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	93.917	495	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902362275.1	s__Collinsella sp902362275	93.767	602	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.48	97.28	0.91	0.88	7	-
GCA_900761945.1	s__Collinsella sp900761945	93.5936	364	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761035.1	s__Collinsella sp900761035	93.5645	397	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546115.1	s__Collinsella sp900546115	93.2912	580	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.55	95.10	0.92	0.84	3	-
GCA_900543945.1	s__Collinsella sp900543945	93.2376	497	819	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.4468	97.82	95.67	0.91	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:43,121] [INFO] GTDB search result was written to GCF_900461335.1_50279_E02_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:43,122] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:43,127] [INFO] DFAST_QC result json was written to GCF_900461335.1_50279_E02_genomic.fna/dqc_result.json
[2024-01-24 15:19:43,127] [INFO] DFAST_QC completed!
[2024-01-24 15:19:43,127] [INFO] Total running time: 0h1m4s