[2023-06-07 22:39:32,508] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:39:32,510] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:39:32,510] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc88396c-d73b-4819-ad1a-257b244f1f1d/dqc_reference
[2023-06-07 22:39:34,321] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:39:34,322] [INFO] Task started: Prodigal
[2023-06-07 22:39:34,322] [INFO] Running command: gunzip -c /var/lib/cwl/stg06ca2bfd-3d34-4579-8db2-1866542080df/GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna.gz | prodigal -d GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/cds.fna -a GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:39:40,324] [INFO] Task succeeded: Prodigal
[2023-06-07 22:39:40,324] [INFO] Task started: HMMsearch
[2023-06-07 22:39:40,325] [INFO] Running command: hmmsearch --tblout GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc88396c-d73b-4819-ad1a-257b244f1f1d/dqc_reference/reference_markers.hmm GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:39:40,572] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:39:40,573] [INFO] Found 6/6 markers.
[2023-06-07 22:39:40,596] [INFO] Query marker FASTA was written to GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/markers.fasta
[2023-06-07 22:39:40,597] [INFO] Task started: Blastn
[2023-06-07 22:39:40,597] [INFO] Running command: blastn -query GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc88396c-d73b-4819-ad1a-257b244f1f1d/dqc_reference/reference_markers.fasta -out GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:39:41,304] [INFO] Task succeeded: Blastn
[2023-06-07 22:39:41,308] [INFO] Selected 15 target genomes.
[2023-06-07 22:39:41,309] [INFO] Target genome list was writen to GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/target_genomes.txt
[2023-06-07 22:39:41,311] [INFO] Task started: fastANI
[2023-06-07 22:39:41,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg06ca2bfd-3d34-4579-8db2-1866542080df/GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna.gz --refList GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/target_genomes.txt --output GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 22:39:47,457] [INFO] Task succeeded: fastANI
[2023-06-07 22:39:47,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc88396c-d73b-4819-ad1a-257b244f1f1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 22:39:47,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc88396c-d73b-4819-ad1a-257b244f1f1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 22:39:47,476] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 22:39:47,476] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 22:39:47,476] [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	94.7623	567	636	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	94.7348	568	636	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	94.6771	572	636	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.0505	225	636	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.9271	238	636	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.898	240	636	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.8085	232	636	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.7739	214	636	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.5671	221	636	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.4982	219	636	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.1848	195	636	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	79.1458	177	636	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 22:39:47,485] [INFO] DFAST Taxonomy check result was written to GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/tc_result.tsv
[2023-06-07 22:39:47,486] [INFO] ===== Taxonomy check completed =====
[2023-06-07 22:39:47,486] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:39:47,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc88396c-d73b-4819-ad1a-257b244f1f1d/dqc_reference/checkm_data
[2023-06-07 22:39:47,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:39:47,516] [INFO] Task started: CheckM
[2023-06-07 22:39:47,517] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/checkm_input GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/checkm_result
[2023-06-07 22:40:10,998] [INFO] Task succeeded: CheckM
[2023-06-07 22:40:11,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 22:40:11,030] [INFO] ===== Completeness check finished =====
[2023-06-07 22:40:11,031] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:40:11,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/markers.fasta)
[2023-06-07 22:40:11,031] [INFO] Task started: Blastn
[2023-06-07 22:40:11,031] [INFO] Running command: blastn -query GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc88396c-d73b-4819-ad1a-257b244f1f1d/dqc_reference/reference_markers_gtdb.fasta -out GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:40:12,381] [INFO] Task succeeded: Blastn
[2023-06-07 22:40:12,384] [INFO] Selected 26 target genomes.
[2023-06-07 22:40:12,384] [INFO] Target genome list was writen to GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:40:12,397] [INFO] Task started: fastANI
[2023-06-07 22:40:12,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg06ca2bfd-3d34-4579-8db2-1866542080df/GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna.gz --refList GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/target_genomes_gtdb.txt --output GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:40:24,097] [INFO] Task succeeded: fastANI
[2023-06-07 22:40:24,120] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 22:40:24,121] [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_900544995.1	s__Collinsella sp900544995	100.0	605	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.93	0.93	2	conclusive
GCF_015670795.1	s__Collinsella aerofaciens_Q	94.8791	572	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1438	95.30	95.30	0.93	0.92	3	-
GCA_018373675.1	s__Collinsella sp018373675	94.8724	545	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0912	N/A	N/A	N/A	N/A	1	-
GCA_018380015.1	s__Collinsella sp018380015	94.7377	559	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1883	96.09	95.27	0.89	0.86	8	-
GCA_900541175.1	s__Collinsella sp900541175	94.7182	555	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2242	N/A	N/A	N/A	N/A	1	-
GCF_005845035.1	s__Collinsella aerofaciens_I	94.6782	560	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.53	95.20	0.90	0.88	4	-
GCA_900540995.1	s__Collinsella sp900540995	94.6309	541	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.96	99.96	0.96	0.96	2	-
GCA_900541065.1	s__Collinsella sp900541065	94.6047	558	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0334	N/A	N/A	N/A	N/A	1	-
GCA_900541285.1	s__Collinsella sp900541285	94.578	465	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.43	95.28	0.84	0.84	3	-
GCA_900539035.1	s__Collinsella sp900539035	94.5775	541	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.92	99.92	0.95	0.95	2	-
GCA_900552185.1	s__Collinsella sp900552185	94.5054	408	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1905	N/A	N/A	N/A	N/A	1	-
GCA_900761085.1	s__Collinsella sp900761085	94.3899	459	636	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	94.3693	483	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552145.1	s__Collinsella sp900552145	94.3651	484	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.82	98.82	0.84	0.84	2	-
GCA_900544425.1	s__Collinsella sp900544425	94.2938	443	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762325.1	s__Collinsella sp900762325	94.2498	544	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554645.1	s__Collinsella sp900554645	94.2058	285	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761995.1	s__Collinsella sp900761995	94.1684	493	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018376905.1	s__Collinsella sp018376905	94.1559	555	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542315.1	s__Collinsella sp900542315	94.1426	538	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541665.1	s__Collinsella sp900541665	94.124	537	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900545055.1	s__Collinsella sp900545055	94.0631	473	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545995.1	s__Collinsella sp900545995	93.7601	455	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546105.1	s__Collinsella sp900546105	93.7038	472	636	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	93.6494	554	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900551605.1	s__Collinsella sp900551605	93.4111	352	636	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.27	95.27	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-07 22:40:24,123] [INFO] GTDB search result was written to GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/result_gtdb.tsv
[2023-06-07 22:40:24,124] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:40:24,131] [INFO] DFAST_QC result json was written to GCA_902461335.1_UHGG-TPA_MGYG-HGUT-00331_genomic.fna/dqc_result.json
[2023-06-07 22:40:24,132] [INFO] DFAST_QC completed!
[2023-06-07 22:40:24,132] [INFO] Total running time: 0h0m52s