[2024-01-24 13:37:40,366] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:40,367] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:40,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg35a90f38-f9c0-4868-a9dd-ed805a6003fd/dqc_reference
[2024-01-24 13:37:41,545] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:41,545] [INFO] Task started: Prodigal
[2024-01-24 13:37:41,546] [INFO] Running command: gunzip -c /var/lib/cwl/stg48339a11-0fe8-41df-97b0-f0ea9319761b/GCF_000382385.1_ASM38238v1_genomic.fna.gz | prodigal -d GCF_000382385.1_ASM38238v1_genomic.fna/cds.fna -a GCF_000382385.1_ASM38238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:57,488] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:57,488] [INFO] Task started: HMMsearch
[2024-01-24 13:37:57,488] [INFO] Running command: hmmsearch --tblout GCF_000382385.1_ASM38238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35a90f38-f9c0-4868-a9dd-ed805a6003fd/dqc_reference/reference_markers.hmm GCF_000382385.1_ASM38238v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:57,701] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:57,702] [INFO] Found 6/6 markers.
[2024-01-24 13:37:57,726] [INFO] Query marker FASTA was written to GCF_000382385.1_ASM38238v1_genomic.fna/markers.fasta
[2024-01-24 13:37:57,726] [INFO] Task started: Blastn
[2024-01-24 13:37:57,726] [INFO] Running command: blastn -query GCF_000382385.1_ASM38238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35a90f38-f9c0-4868-a9dd-ed805a6003fd/dqc_reference/reference_markers.fasta -out GCF_000382385.1_ASM38238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:58,276] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:58,278] [INFO] Selected 15 target genomes.
[2024-01-24 13:37:58,278] [INFO] Target genome list was writen to GCF_000382385.1_ASM38238v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:58,286] [INFO] Task started: fastANI
[2024-01-24 13:37:58,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg48339a11-0fe8-41df-97b0-f0ea9319761b/GCF_000382385.1_ASM38238v1_genomic.fna.gz --refList GCF_000382385.1_ASM38238v1_genomic.fna/target_genomes.txt --output GCF_000382385.1_ASM38238v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:07,410] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:07,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35a90f38-f9c0-4868-a9dd-ed805a6003fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:07,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35a90f38-f9c0-4868-a9dd-ed805a6003fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:07,419] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:38:07,420] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:07,420] [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
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	100.0	1069	1074	95	conclusive
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	99.8928	1022	1074	95	conclusive
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	81.7548	120	1074	95	below_threshold
Prevotella oris	strain=NCTC13071	GCA_900637655.1	28135	28135	type	True	81.4273	459	1074	95	below_threshold
Prevotella oris	strain=JCM 12252	GCA_000613505.1	28135	28135	type	True	81.3934	441	1074	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	81.3767	449	1074	95	below_threshold
Prevotella salivae	strain=DSM 15606	GCA_000185845.1	228604	228604	type	True	80.1886	279	1074	95	below_threshold
Prevotella oulorum	strain=ATCC 43324	GCA_900167385.1	28136	28136	type	True	80.0815	210	1074	95	below_threshold
Prevotella herbatica	strain=WR041	GCA_017347605.1	2801997	2801997	type	True	78.2724	72	1074	95	below_threshold
Prevotella paludivivens	strain=JCM 13650	GCA_000613605.1	185294	185294	type	True	77.8337	78	1074	95	below_threshold
Prevotella paludivivens	strain=DSM 17968	GCA_000373185.1	185294	185294	type	True	77.8026	78	1074	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.6269	61	1074	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.2675	78	1074	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:07,421] [INFO] DFAST Taxonomy check result was written to GCF_000382385.1_ASM38238v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:07,422] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:07,422] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:07,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35a90f38-f9c0-4868-a9dd-ed805a6003fd/dqc_reference/checkm_data
[2024-01-24 13:38:07,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:07,455] [INFO] Task started: CheckM
[2024-01-24 13:38:07,455] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000382385.1_ASM38238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000382385.1_ASM38238v1_genomic.fna/checkm_input GCF_000382385.1_ASM38238v1_genomic.fna/checkm_result
[2024-01-24 13:38:53,261] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:53,262] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:53,277] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:53,277] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:53,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000382385.1_ASM38238v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:53,278] [INFO] Task started: Blastn
[2024-01-24 13:38:53,278] [INFO] Running command: blastn -query GCF_000382385.1_ASM38238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35a90f38-f9c0-4868-a9dd-ed805a6003fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000382385.1_ASM38238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:54,040] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:54,042] [INFO] Selected 20 target genomes.
[2024-01-24 13:38:54,042] [INFO] Target genome list was writen to GCF_000382385.1_ASM38238v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:54,058] [INFO] Task started: fastANI
[2024-01-24 13:38:54,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg48339a11-0fe8-41df-97b0-f0ea9319761b/GCF_000382385.1_ASM38238v1_genomic.fna.gz --refList GCF_000382385.1_ASM38238v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000382385.1_ASM38238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:05,618] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:05,627] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:05,627] [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_000382385.1	s__Prevotella maculosa	100.0	1069	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.13	97.00	0.93	0.87	4	conclusive
GCF_900637655.1	s__Prevotella oris	81.4245	461	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.96	97.06	0.90	0.82	10	-
GCF_000599605.1	s__Prevotella sp000599605	81.4023	173	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.66	96.63	0.93	0.92	3	-
GCF_000613785.1	s__Prevotella oulorum	80.2847	203	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.00	96.91	0.92	0.84	5	-
GCF_000185845.1	s__Prevotella salivae	80.1978	278	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.60	96.70	0.94	0.87	27	-
GCF_001553265.1	s__Prevotella sp001553265	78.7487	104	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.33	99.33	0.90	0.90	2	-
GCF_000184945.1	s__Prevotella buccae	78.6397	151	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCF_017347605.1	s__Prevotella sp017347605	78.3424	72	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426585.1	s__Prevotella baroniae	77.9098	139	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.79	98.01	0.95	0.92	4	-
GCF_000373185.1	s__Prevotella paludivivens	77.8026	78	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.98	0.99	0.99	2	-
GCA_018053665.1	s__Prevotella sp018053665	77.5465	74	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.38	99.32	0.87	0.85	3	-
GCA_018054505.1	s__Prevotella sp018054505	76.8802	55	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.05	98.05	0.52	0.52	2	-
GCF_013166545.1	s__Prevotella sp013166545	76.6135	65	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.93	99.88	0.98	0.97	6	-
GCA_900544495.1	s__Prevotella sp900544495	76.586	58	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_902769705.1	s__Prevotella sp902769705	76.2724	66	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.53	0.84	0.80	3	-
GCA_900549175.1	s__Prevotella sp900549175	76.0484	51	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.84	99.84	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:05,629] [INFO] GTDB search result was written to GCF_000382385.1_ASM38238v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:05,629] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:05,632] [INFO] DFAST_QC result json was written to GCF_000382385.1_ASM38238v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:05,632] [INFO] DFAST_QC completed!
[2024-01-24 13:39:05,632] [INFO] Total running time: 0h1m25s