[2024-01-24 12:40:06,740] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:06,744] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:06,744] [INFO] DQC Reference Directory: /var/lib/cwl/stg66cfd981-9173-43c4-bd5c-710483cad844/dqc_reference
[2024-01-24 12:40:08,027] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:08,028] [INFO] Task started: Prodigal
[2024-01-24 12:40:08,028] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5280389-cc97-4134-8bc3-2844b36470de/GCF_000613765.1_ASM61376v1_genomic.fna.gz | prodigal -d GCF_000613765.1_ASM61376v1_genomic.fna/cds.fna -a GCF_000613765.1_ASM61376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:16,265] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:16,266] [INFO] Task started: HMMsearch
[2024-01-24 12:40:16,266] [INFO] Running command: hmmsearch --tblout GCF_000613765.1_ASM61376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66cfd981-9173-43c4-bd5c-710483cad844/dqc_reference/reference_markers.hmm GCF_000613765.1_ASM61376v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:16,458] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:16,459] [INFO] Found 6/6 markers.
[2024-01-24 12:40:16,483] [INFO] Query marker FASTA was written to GCF_000613765.1_ASM61376v1_genomic.fna/markers.fasta
[2024-01-24 12:40:16,484] [INFO] Task started: Blastn
[2024-01-24 12:40:16,484] [INFO] Running command: blastn -query GCF_000613765.1_ASM61376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66cfd981-9173-43c4-bd5c-710483cad844/dqc_reference/reference_markers.fasta -out GCF_000613765.1_ASM61376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:17,061] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:17,065] [INFO] Selected 15 target genomes.
[2024-01-24 12:40:17,065] [INFO] Target genome list was writen to GCF_000613765.1_ASM61376v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:17,071] [INFO] Task started: fastANI
[2024-01-24 12:40:17,072] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5280389-cc97-4134-8bc3-2844b36470de/GCF_000613765.1_ASM61376v1_genomic.fna.gz --refList GCF_000613765.1_ASM61376v1_genomic.fna/target_genomes.txt --output GCF_000613765.1_ASM61376v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:24,047] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:24,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66cfd981-9173-43c4-bd5c-710483cad844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:24,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66cfd981-9173-43c4-bd5c-710483cad844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:24,059] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:24,059] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:24,060] [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 amnii	strain=JCM 14753	GCA_000613765.1	419005	419005	type	True	100.0	715	720	95	conclusive
Prevotella amnii	strain=DSM 23384	GCA_000378745.1	419005	419005	type	True	99.9436	717	720	95	conclusive
Prevotella ihumii	strain=Marseille-P3385	GCA_900155655.1	1917878	1917878	type	True	82.9211	143	720	95	below_threshold
Prevotella disiens	strain=NCTC11157	GCA_900454955.1	28130	28130	type	True	82.3737	126	720	95	below_threshold
Prevotella bivia	strain=DSM 20514	GCA_000262545.1	28125	28125	type	True	81.0965	307	720	95	below_threshold
Prevotella bivia	strain=JCVIHMP010	GCA_000177315.1	28125	28125	type	True	80.9575	287	720	95	below_threshold
Prevotella disiens	strain=ATCC 29426	GCA_000467875.1	28130	28130	type	True	80.9153	99	720	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	80.5532	88	720	95	below_threshold
Prevotella jejuni	strain=DSM 26989	GCA_900187995.1	1177574	1177574	type	True	80.2145	92	720	95	below_threshold
Prevotella histicola	strain=JCM 15637	GCA_000613925.1	470565	470565	type	True	79.7703	90	720	95	below_threshold
Prevotella bryantii	strain=B14	GCA_022024235.1	77095	77095	type	True	78.053	51	720	95	below_threshold
Prevotella bryantii	strain=DSM 11371	GCA_019973295.1	77095	77095	type	True	78.0173	51	720	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:24,062] [INFO] DFAST Taxonomy check result was written to GCF_000613765.1_ASM61376v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:24,063] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:24,063] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:24,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66cfd981-9173-43c4-bd5c-710483cad844/dqc_reference/checkm_data
[2024-01-24 12:40:24,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:24,091] [INFO] Task started: CheckM
[2024-01-24 12:40:24,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613765.1_ASM61376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613765.1_ASM61376v1_genomic.fna/checkm_input GCF_000613765.1_ASM61376v1_genomic.fna/checkm_result
[2024-01-24 12:40:51,500] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:51,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:51,518] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:51,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:51,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613765.1_ASM61376v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:51,519] [INFO] Task started: Blastn
[2024-01-24 12:40:51,519] [INFO] Running command: blastn -query GCF_000613765.1_ASM61376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66cfd981-9173-43c4-bd5c-710483cad844/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613765.1_ASM61376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:52,294] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:52,297] [INFO] Selected 26 target genomes.
[2024-01-24 12:40:52,298] [INFO] Target genome list was writen to GCF_000613765.1_ASM61376v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:52,314] [INFO] Task started: fastANI
[2024-01-24 12:40:52,315] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5280389-cc97-4134-8bc3-2844b36470de/GCF_000613765.1_ASM61376v1_genomic.fna.gz --refList GCF_000613765.1_ASM61376v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613765.1_ASM61376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:05,452] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:05,464] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:05,464] [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_000378745.1	s__Prevotella amnii	99.9436	717	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.70	98.21	0.90	0.86	5	conclusive
GCF_000430525.1	s__Prevotella corporis	83.8263	100	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.63	97.78	0.92	0.87	4	-
GCF_900155655.1	s__Prevotella ihumii	82.9277	142	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018127785.1	s__Prevotella scopos	81.6452	101	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	4	-
GCF_000262545.1	s__Prevotella bivia	81.1037	306	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.82	98.45	0.91	0.86	8	-
GCF_003977605.1	s__Prevotella koreensis	80.8499	57	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262015.1	s__Prevotella fusca	80.6217	87	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_900187995.1	s__Prevotella jejuni	80.2145	92	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.57	0.92	0.88	7	-
GCF_001953955.1	s__Prevotella intermedia	80.0748	71	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.13	0.88	0.83	34	-
GCF_000377625.1	s__Prevotella veroralis	79.9997	91	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.76	96.65	0.91	0.86	4	-
GCF_000613925.1	s__Prevotella histicola	79.7703	90	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.82	97.59	0.91	0.86	21	-
GCF_000614025.1	s__Prevotella aurantiaca	79.4851	86	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.47	98.39	0.93	0.91	4	-
GCF_000144405.1	s__Prevotella melaninogenica	78.5356	87	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_018127965.1	s__Prevotella melaninogenica_B	77.6608	82	720	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.77	95.72	0.91	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:05,466] [INFO] GTDB search result was written to GCF_000613765.1_ASM61376v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:05,466] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:05,470] [INFO] DFAST_QC result json was written to GCF_000613765.1_ASM61376v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:05,470] [INFO] DFAST_QC completed!
[2024-01-24 12:41:05,471] [INFO] Total running time: 0h0m59s