[2023-06-07 21:33:32,854] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:33:32,858] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:33:32,858] [INFO] DQC Reference Directory: /var/lib/cwl/stgfee4ef3f-485e-43b0-b35b-c5a0e62cb8c5/dqc_reference
[2023-06-07 21:33:35,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:33:35,726] [INFO] Task started: Prodigal
[2023-06-07 21:33:35,726] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a1675b9-3762-4330-885f-9297ea9244c0/GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna.gz | prodigal -d GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/cds.fna -a GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:33:40,999] [INFO] Task succeeded: Prodigal
[2023-06-07 21:33:41,000] [INFO] Task started: HMMsearch
[2023-06-07 21:33:41,000] [INFO] Running command: hmmsearch --tblout GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfee4ef3f-485e-43b0-b35b-c5a0e62cb8c5/dqc_reference/reference_markers.hmm GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:33:41,234] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:33:41,236] [INFO] Found 6/6 markers.
[2023-06-07 21:33:41,262] [INFO] Query marker FASTA was written to GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/markers.fasta
[2023-06-07 21:33:41,262] [INFO] Task started: Blastn
[2023-06-07 21:33:41,262] [INFO] Running command: blastn -query GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/markers.fasta -db /var/lib/cwl/stgfee4ef3f-485e-43b0-b35b-c5a0e62cb8c5/dqc_reference/reference_markers.fasta -out GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:33:41,977] [INFO] Task succeeded: Blastn
[2023-06-07 21:33:41,982] [INFO] Selected 14 target genomes.
[2023-06-07 21:33:41,983] [INFO] Target genome list was writen to GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/target_genomes.txt
[2023-06-07 21:33:41,985] [INFO] Task started: fastANI
[2023-06-07 21:33:41,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a1675b9-3762-4330-885f-9297ea9244c0/GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna.gz --refList GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/target_genomes.txt --output GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:33:49,567] [INFO] Task succeeded: fastANI
[2023-06-07 21:33:49,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfee4ef3f-485e-43b0-b35b-c5a0e62cb8c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:33:49,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfee4ef3f-485e-43b0-b35b-c5a0e62cb8c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:33:49,578] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:33:49,578] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 21:33:49,578] [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	93.6937	441	509	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	93.6305	449	509	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	93.6092	450	509	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.6383	182	509	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	80.4496	176	509	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.2569	203	509	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.9612	193	509	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.9388	177	509	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.4906	176	509	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.3558	159	509	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 21:33:49,584] [INFO] DFAST Taxonomy check result was written to GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/tc_result.tsv
[2023-06-07 21:33:49,585] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:33:49,585] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:33:49,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfee4ef3f-485e-43b0-b35b-c5a0e62cb8c5/dqc_reference/checkm_data
[2023-06-07 21:33:49,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:33:49,616] [INFO] Task started: CheckM
[2023-06-07 21:33:49,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/checkm_input GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/checkm_result
[2023-06-07 21:34:12,104] [INFO] Task succeeded: CheckM
[2023-06-07 21:34:12,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-07 21:34:12,134] [INFO] ===== Completeness check finished =====
[2023-06-07 21:34:12,135] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:34:12,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/markers.fasta)
[2023-06-07 21:34:12,136] [INFO] Task started: Blastn
[2023-06-07 21:34:12,136] [INFO] Running command: blastn -query GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/markers.fasta -db /var/lib/cwl/stgfee4ef3f-485e-43b0-b35b-c5a0e62cb8c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:34:13,504] [INFO] Task succeeded: Blastn
[2023-06-07 21:34:13,507] [INFO] Selected 29 target genomes.
[2023-06-07 21:34:13,507] [INFO] Target genome list was writen to GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:34:13,554] [INFO] Task started: fastANI
[2023-06-07 21:34:13,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a1675b9-3762-4330-885f-9297ea9244c0/GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna.gz --refList GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/target_genomes_gtdb.txt --output GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:34:25,045] [INFO] Task succeeded: fastANI
[2023-06-07 21:34:25,074] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 21:34:25,075] [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_900549245.1	s__Collinsella sp900549245	99.9802	486	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015554145.1	s__Collinsella aerofaciens_AA	94.6885	455	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002736145.1	s__Collinsella aerofaciens_A	94.6682	448	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900768435.1	s__Collinsella sp900768435	94.6494	443	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015561195.1	s__Collinsella aerofaciens_AC	94.625	457	509	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	94.5265	449	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.84	99.84	0.98	0.98	2	-
GCF_003436275.1	s__Collinsella sp003436275	94.5186	454	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.89	95.08	0.88	0.83	16	-
GCA_900542175.1	s__Collinsella sp900542175	94.4734	427	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0662	N/A	N/A	N/A	N/A	1	-
GCA_905215385.1	s__Collinsella sp905215385	94.3814	452	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2035	95.42	95.23	0.87	0.82	17	-
GCA_900541645.1	s__Collinsella sp900541645	94.375	435	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.32	95.32	0.85	0.85	2	-
GCA_902363125.1	s__Collinsella sp902363125	94.3438	449	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.02	96.02	0.87	0.87	2	-
GCA_018368345.1	s__Collinsella sp018368345	94.3187	449	509	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	94.3156	437	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003469205.1	s__Collinsella sp003469205	94.3024	438	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.74	95.06	0.88	0.84	17	-
GCA_900552995.1	s__Collinsella sp900552995	94.2011	254	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.58	95.21	0.80	0.68	3	-
GCA_905214105.1	s__Collinsella sp905214105	94.1021	452	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544755.1	s__Collinsella sp900544755	94.0294	414	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0835	100.00	100.00	0.97	0.97	2	-
GCA_900757185.1	s__Collinsella sp900757185	93.9624	426	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.15	95.15	0.87	0.87	2	-
GCF_001405375.1	s__Collinsella aerofaciens_F	93.8989	449	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2147	95.33	95.22	0.89	0.87	8	-
GCA_900549745.1	s__Collinsella sp900549745	93.8597	400	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1078	95.40	95.40	0.87	0.87	2	-
GCA_900541135.1	s__Collinsella sp900541135	93.7622	440	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552705.1	s__Collinsella sp900552705	93.7347	372	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552425.1	s__Collinsella sp900552425	93.6988	339	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.79	96.79	0.91	0.91	2	-
GCA_900553215.1	s__Collinsella sp900553215	93.6355	315	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.53	99.53	0.82	0.82	2	-
GCA_900547805.1	s__Collinsella sp900547805	93.6334	394	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757385.1	s__Collinsella sp900757385	93.6323	366	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547505.1	s__Collinsella sp900547505	93.525	356	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545905.1	s__Collinsella sp900545905	93.5079	334	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554495.1	s__Collinsella sp900554495	93.0857	348	509	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 21:34:25,077] [INFO] GTDB search result was written to GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/result_gtdb.tsv
[2023-06-07 21:34:25,077] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:34:25,082] [INFO] DFAST_QC result json was written to GCA_902461395.1_UHGG-TPA_MGYG-HGUT-00324_genomic.fna/dqc_result.json
[2023-06-07 21:34:25,083] [INFO] DFAST_QC completed!
[2023-06-07 21:34:25,083] [INFO] Total running time: 0h0m52s