[2023-06-16 19:18:58,876] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:18:58,878] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:18:58,878] [INFO] DQC Reference Directory: /var/lib/cwl/stg8575ecaf-8e95-4576-9f1e-ede09533c6f1/dqc_reference
[2023-06-16 19:19:00,002] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:19:00,003] [INFO] Task started: Prodigal
[2023-06-16 19:19:00,003] [INFO] Running command: gunzip -c /var/lib/cwl/stg98fa9e3e-86e7-4063-9e39-994748947742/GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna.gz | prodigal -d GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/cds.fna -a GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:19:04,798] [INFO] Task succeeded: Prodigal
[2023-06-16 19:19:04,799] [INFO] Task started: HMMsearch
[2023-06-16 19:19:04,799] [INFO] Running command: hmmsearch --tblout GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8575ecaf-8e95-4576-9f1e-ede09533c6f1/dqc_reference/reference_markers.hmm GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:19:04,994] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:19:04,995] [INFO] Found 6/6 markers.
[2023-06-16 19:19:05,014] [INFO] Query marker FASTA was written to GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/markers.fasta
[2023-06-16 19:19:05,014] [INFO] Task started: Blastn
[2023-06-16 19:19:05,014] [INFO] Running command: blastn -query GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/markers.fasta -db /var/lib/cwl/stg8575ecaf-8e95-4576-9f1e-ede09533c6f1/dqc_reference/reference_markers.fasta -out GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:19:05,679] [INFO] Task succeeded: Blastn
[2023-06-16 19:19:05,681] [INFO] Selected 14 target genomes.
[2023-06-16 19:19:05,682] [INFO] Target genome list was writen to GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/target_genomes.txt
[2023-06-16 19:19:05,682] [INFO] Task started: fastANI
[2023-06-16 19:19:05,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg98fa9e3e-86e7-4063-9e39-994748947742/GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna.gz --refList GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/target_genomes.txt --output GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:19:11,950] [INFO] Task succeeded: fastANI
[2023-06-16 19:19:11,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8575ecaf-8e95-4576-9f1e-ede09533c6f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:19:11,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8575ecaf-8e95-4576-9f1e-ede09533c6f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:19:11,963] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:19:11,963] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:19:11,963] [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	94.7377	489	551	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	94.6721	492	551	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	94.6626	499	551	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.4822	175	551	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.0768	215	551	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.568	207	551	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.501	185	551	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.3496	195	551	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	79.2402	138	551	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.0764	172	551	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:19:11,966] [INFO] DFAST Taxonomy check result was written to GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/tc_result.tsv
[2023-06-16 19:19:11,966] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:19:11,967] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:19:11,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8575ecaf-8e95-4576-9f1e-ede09533c6f1/dqc_reference/checkm_data
[2023-06-16 19:19:11,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:19:11,990] [INFO] Task started: CheckM
[2023-06-16 19:19:11,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/checkm_input GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/checkm_result
[2023-06-16 19:19:31,190] [INFO] Task succeeded: CheckM
[2023-06-16 19:19:31,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.08%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:19:31,215] [INFO] ===== Completeness check finished =====
[2023-06-16 19:19:31,215] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:19:31,216] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/markers.fasta)
[2023-06-16 19:19:31,216] [INFO] Task started: Blastn
[2023-06-16 19:19:31,216] [INFO] Running command: blastn -query GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/markers.fasta -db /var/lib/cwl/stg8575ecaf-8e95-4576-9f1e-ede09533c6f1/dqc_reference/reference_markers_gtdb.fasta -out GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:19:32,493] [INFO] Task succeeded: Blastn
[2023-06-16 19:19:32,498] [INFO] Selected 30 target genomes.
[2023-06-16 19:19:32,498] [INFO] Target genome list was writen to GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:19:32,514] [INFO] Task started: fastANI
[2023-06-16 19:19:32,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg98fa9e3e-86e7-4063-9e39-994748947742/GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna.gz --refList GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/target_genomes_gtdb.txt --output GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:19:44,732] [INFO] Task succeeded: fastANI
[2023-06-16 19:19:44,750] [INFO] Found 30 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:19:44,750] [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_900541235.1	s__Collinsella sp900541235	95.0247	474	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.02	95.02	0.86	0.86	2	conclusive
GCA_018380015.1	s__Collinsella sp018380015	94.9452	481	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1883	96.09	95.27	0.89	0.86	8	-
GCA_900752015.1	s__Collinsella sp900752015	94.9199	451	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1642	99.95	99.95	0.93	0.93	2	-
GCA_008671135.1	s__Collinsella aerofaciens_J	94.909	485	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2147	97.21	95.28	0.90	0.82	6	-
GCA_900542165.1	s__Collinsella sp900542165	94.865	485	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0912	95.41	95.20	0.86	0.82	3	-
GCF_010509075.1	s__Collinsella aerofaciens	94.6721	492	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.99	99.98	1.00	0.99	4	-
GCA_900541185.1	s__Collinsella sp900541185	94.5737	453	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.043	N/A	N/A	N/A	N/A	1	-
GCF_003438495.1	s__Collinsella sp003438495	94.4589	492	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_905216145.1	s__Collinsella sp905216145	94.4103	484	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545605.1	s__Collinsella sp900545605	94.3391	452	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541885.1	s__Collinsella sp900541885	94.3326	474	551	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	94.2901	447	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.87	98.87	0.87	0.87	2	-
GCA_900545505.1	s__Collinsella sp900545505	94.2881	333	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0349	N/A	N/A	N/A	N/A	1	-
GCA_900541025.1	s__Collinsella sp900541025	94.2877	472	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540895.1	s__Collinsella sp900540895	94.2287	483	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.25	95.25	0.87	0.87	2	-
GCA_900547765.1	s__Collinsella sp900547765	94.1056	474	551	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	94.0418	354	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552295.1	s__Collinsella sp900552295	93.9656	338	551	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	93.8701	337	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549335.1	s__Collinsella sp900549335	93.8512	327	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549185.1	s__Collinsella sp900549185	93.8409	420	551	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	93.5343	466	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.84	99.84	0.98	0.98	2	-
GCF_003465825.1	s__Collinsella sp003465825	93.4525	466	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.4968	95.86	95.69	0.87	0.85	6	-
GCA_900552995.1	s__Collinsella sp900552995	93.4267	262	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.58	95.21	0.80	0.68	3	-
GCA_900555515.1	s__Collinsella sp900555515	93.3742	350	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544225.1	s__Collinsella sp900544225	93.1396	421	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.82	95.63	0.93	0.89	3	-
GCA_900540875.1	s__Collinsella sp900540875	93.0037	470	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.98	0.98	2	-
GCA_900552425.1	s__Collinsella sp900552425	92.8456	349	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.79	96.79	0.91	0.91	2	-
GCA_900548935.1	s__Collinsella sp900548935	92.7671	390	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900756725.1	s__Collinsella sp900756725	92.3806	396	551	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.39	95.39	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-16 19:19:44,756] [INFO] GTDB search result was written to GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/result_gtdb.tsv
[2023-06-16 19:19:44,757] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:19:44,760] [INFO] DFAST_QC result json was written to GCA_905207425.1_ERR414303-mag-bin.14_genomic.fna/dqc_result.json
[2023-06-16 19:19:44,761] [INFO] DFAST_QC completed!
[2023-06-16 19:19:44,761] [INFO] Total running time: 0h0m46s