[2023-06-30 15:20:37,730] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:20:37,739] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:20:37,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a4960b0-fab8-436c-8258-aafbb6f8bc60/dqc_reference
[2023-06-30 15:20:40,035] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:20:40,037] [INFO] Task started: Prodigal
[2023-06-30 15:20:40,038] [INFO] Running command: gunzip -c /var/lib/cwl/stg97a08b35-01fc-4632-883e-0b37c1c618fb/GCA_900762955.1_SRS1596784_11_genomic.fna.gz | prodigal -d GCA_900762955.1_SRS1596784_11_genomic.fna/cds.fna -a GCA_900762955.1_SRS1596784_11_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:20:46,606] [INFO] Task succeeded: Prodigal
[2023-06-30 15:20:46,607] [INFO] Task started: HMMsearch
[2023-06-30 15:20:46,607] [INFO] Running command: hmmsearch --tblout GCA_900762955.1_SRS1596784_11_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a4960b0-fab8-436c-8258-aafbb6f8bc60/dqc_reference/reference_markers.hmm GCA_900762955.1_SRS1596784_11_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:20:46,814] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:20:46,816] [INFO] Found 6/6 markers.
[2023-06-30 15:20:46,839] [INFO] Query marker FASTA was written to GCA_900762955.1_SRS1596784_11_genomic.fna/markers.fasta
[2023-06-30 15:20:46,839] [INFO] Task started: Blastn
[2023-06-30 15:20:46,840] [INFO] Running command: blastn -query GCA_900762955.1_SRS1596784_11_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a4960b0-fab8-436c-8258-aafbb6f8bc60/dqc_reference/reference_markers.fasta -out GCA_900762955.1_SRS1596784_11_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:20:47,574] [INFO] Task succeeded: Blastn
[2023-06-30 15:20:47,579] [INFO] Selected 15 target genomes.
[2023-06-30 15:20:47,579] [INFO] Target genome list was writen to GCA_900762955.1_SRS1596784_11_genomic.fna/target_genomes.txt
[2023-06-30 15:20:47,581] [INFO] Task started: fastANI
[2023-06-30 15:20:47,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg97a08b35-01fc-4632-883e-0b37c1c618fb/GCA_900762955.1_SRS1596784_11_genomic.fna.gz --refList GCA_900762955.1_SRS1596784_11_genomic.fna/target_genomes.txt --output GCA_900762955.1_SRS1596784_11_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:20:55,228] [INFO] Task succeeded: fastANI
[2023-06-30 15:20:55,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a4960b0-fab8-436c-8258-aafbb6f8bc60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:20:55,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a4960b0-fab8-436c-8258-aafbb6f8bc60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:20:55,244] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:20:55,244] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:20:55,244] [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	92.5174	580	693	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	92.4666	578	693	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	92.454	583	693	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.3826	237	693	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.932	245	693	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.7017	221	693	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.6374	280	693	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.4767	225	693	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.4022	228	693	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.1811	204	693	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	78.5531	137	693	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:20:55,246] [INFO] DFAST Taxonomy check result was written to GCA_900762955.1_SRS1596784_11_genomic.fna/tc_result.tsv
[2023-06-30 15:20:55,247] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:20:55,247] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:20:55,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a4960b0-fab8-436c-8258-aafbb6f8bc60/dqc_reference/checkm_data
[2023-06-30 15:20:55,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:20:55,271] [INFO] Task started: CheckM
[2023-06-30 15:20:55,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900762955.1_SRS1596784_11_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900762955.1_SRS1596784_11_genomic.fna/checkm_input GCA_900762955.1_SRS1596784_11_genomic.fna/checkm_result
[2023-06-30 15:21:19,432] [INFO] Task succeeded: CheckM
[2023-06-30 15:21:19,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:21:19,458] [INFO] ===== Completeness check finished =====
[2023-06-30 15:21:19,458] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:21:19,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900762955.1_SRS1596784_11_genomic.fna/markers.fasta)
[2023-06-30 15:21:19,460] [INFO] Task started: Blastn
[2023-06-30 15:21:19,460] [INFO] Running command: blastn -query GCA_900762955.1_SRS1596784_11_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a4960b0-fab8-436c-8258-aafbb6f8bc60/dqc_reference/reference_markers_gtdb.fasta -out GCA_900762955.1_SRS1596784_11_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:21:20,788] [INFO] Task succeeded: Blastn
[2023-06-30 15:21:20,794] [INFO] Selected 32 target genomes.
[2023-06-30 15:21:20,794] [INFO] Target genome list was writen to GCA_900762955.1_SRS1596784_11_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:21:20,811] [INFO] Task started: fastANI
[2023-06-30 15:21:20,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg97a08b35-01fc-4632-883e-0b37c1c618fb/GCA_900762955.1_SRS1596784_11_genomic.fna.gz --refList GCA_900762955.1_SRS1596784_11_genomic.fna/target_genomes_gtdb.txt --output GCA_900762955.1_SRS1596784_11_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:21:34,854] [INFO] Task succeeded: fastANI
[2023-06-30 15:21:34,880] [INFO] Found 32 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 15:21:34,881] [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_900549085.1	s__Collinsella sp900549085	95.025	559	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.95	99.95	0.97	0.97	2	conclusive
GCA_900542085.1	s__Collinsella sp900542085	94.9042	581	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.96	0.96	2	-
GCA_900541195.1	s__Collinsella sp900541195	94.7453	562	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541695.1	s__Collinsella sp900541695	94.7069	579	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.64	95.64	0.91	0.91	2	-
GCA_900555955.1	s__Collinsella sp900555955	93.931	289	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.54	99.54	0.80	0.80	2	-
GCA_905216075.1	s__Collinsella sp905216075	93.8036	400	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900752545.1	s__Collinsella sp900752545	93.2309	524	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.97	99.97	0.93	0.93	2	-
GCA_900752215.1	s__Collinsella sp900752215	92.9871	484	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0875	99.95	99.95	0.94	0.94	2	-
GCA_900541745.1	s__Collinsella sp900541745	92.9222	570	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.25	95.02	0.88	0.85	9	-
GCA_900544865.1	s__Collinsella sp900544865	92.8442	551	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905209765.1	s__Collinsella sp905209765	92.8353	477	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018785245.1	s__Collinsella aerofaciens_AD	92.7579	566	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1928	N/A	N/A	N/A	N/A	1	-
GCA_900754075.1	s__Collinsella sp900754075	92.6782	498	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.97	99.97	0.96	0.96	2	-
GCA_900752015.1	s__Collinsella sp900752015	92.64	527	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1642	99.95	99.95	0.93	0.93	2	-
GCA_014871665.1	s__Collinsella sp014871665	92.6254	502	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1702	95.19	95.19	0.85	0.85	2	-
GCA_900541725.1	s__Collinsella sp900541725	92.5501	547	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900549745.1	s__Collinsella sp900549745	92.5418	507	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1078	95.40	95.40	0.87	0.87	2	-
GCF_019041915.1	s__Collinsella sp019041915	92.532	582	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.145	96.63	95.48	0.93	0.87	6	-
GCA_900552385.1	s__Collinsella sp900552385	92.4763	445	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1029	95.27	95.27	0.73	0.73	2	-
GCA_900751665.1	s__Collinsella sp900751665	92.4715	414	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.75	99.75	0.87	0.87	2	-
GCA_905216175.1	s__Collinsella sp905216175	92.4463	474	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540095.1	s__Collinsella sp900540095	92.4099	480	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.82	99.82	0.89	0.89	2	-
GCA_900545505.1	s__Collinsella sp900545505	92.3784	362	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0349	N/A	N/A	N/A	N/A	1	-
GCA_900754745.1	s__Collinsella sp900754745	92.3056	499	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.56	95.20	0.85	0.80	3	-
GCA_900552345.1	s__Collinsella sp900552345	92.2747	341	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215275.1	s__Collinsella sp905215275	92.2334	437	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542125.1	s__Collinsella sp900542125	92.1399	543	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544725.1	s__Collinsella sp900544725	92.0589	532	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757705.1	s__Collinsella sp900757705	92.0012	454	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.54	95.54	0.87	0.87	2	-
GCA_900554325.1	s__Collinsella sp900554325	91.941	454	693	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	91.7566	409	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556285.1	s__Collinsella sp900556285	91.4176	309	693	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 15:21:34,883] [INFO] GTDB search result was written to GCA_900762955.1_SRS1596784_11_genomic.fna/result_gtdb.tsv
[2023-06-30 15:21:34,883] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:21:34,888] [INFO] DFAST_QC result json was written to GCA_900762955.1_SRS1596784_11_genomic.fna/dqc_result.json
[2023-06-30 15:21:34,889] [INFO] DFAST_QC completed!
[2023-06-30 15:21:34,889] [INFO] Total running time: 0h0m57s