[2024-01-24 13:37:13,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:13,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:13,589] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf0d9cd6-d820-4475-a85f-aedea444843d/dqc_reference
[2024-01-24 13:37:14,802] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:14,803] [INFO] Task started: Prodigal
[2024-01-24 13:37:14,803] [INFO] Running command: gunzip -c /var/lib/cwl/stge3f0407a-0802-4f17-9c40-340daf26243d/GCF_000613785.1_ASM61378v1_genomic.fna.gz | prodigal -d GCF_000613785.1_ASM61378v1_genomic.fna/cds.fna -a GCF_000613785.1_ASM61378v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:32,270] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:32,270] [INFO] Task started: HMMsearch
[2024-01-24 13:37:32,271] [INFO] Running command: hmmsearch --tblout GCF_000613785.1_ASM61378v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf0d9cd6-d820-4475-a85f-aedea444843d/dqc_reference/reference_markers.hmm GCF_000613785.1_ASM61378v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:32,535] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:32,536] [INFO] Found 6/6 markers.
[2024-01-24 13:37:32,564] [INFO] Query marker FASTA was written to GCF_000613785.1_ASM61378v1_genomic.fna/markers.fasta
[2024-01-24 13:37:32,564] [INFO] Task started: Blastn
[2024-01-24 13:37:32,564] [INFO] Running command: blastn -query GCF_000613785.1_ASM61378v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf0d9cd6-d820-4475-a85f-aedea444843d/dqc_reference/reference_markers.fasta -out GCF_000613785.1_ASM61378v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:33,184] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:33,187] [INFO] Selected 20 target genomes.
[2024-01-24 13:37:33,188] [INFO] Target genome list was writen to GCF_000613785.1_ASM61378v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:33,226] [INFO] Task started: fastANI
[2024-01-24 13:37:33,226] [INFO] Running command: fastANI --query /var/lib/cwl/stge3f0407a-0802-4f17-9c40-340daf26243d/GCF_000613785.1_ASM61378v1_genomic.fna.gz --refList GCF_000613785.1_ASM61378v1_genomic.fna/target_genomes.txt --output GCF_000613785.1_ASM61378v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:44,183] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:44,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf0d9cd6-d820-4475-a85f-aedea444843d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:44,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf0d9cd6-d820-4475-a85f-aedea444843d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:44,197] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:44,198] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:44,198] [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 oulorum	strain=JCM 14966	GCA_000613785.1	28136	28136	type	True	100.0	872	876	95	conclusive
Prevotella oulorum	strain=ATCC 43324	GCA_900167385.1	28136	28136	type	True	99.9566	866	876	95	conclusive
Prevotella saccharolytica	strain=JCM 17484	GCA_000614205.1	633701	633701	type	True	82.2924	75	876	95	below_threshold
Prevotella oris	strain=NCTC13071	GCA_900637655.1	28135	28135	type	True	80.6105	202	876	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	80.3883	208	876	95	below_threshold
Prevotella aurantiaca	strain=JCM 15754	GCA_000614025.1	596085	596085	type	True	80.291	68	876	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	80.2881	199	876	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	80.2812	70	876	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	80.1962	105	876	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	80.046	195	876	95	below_threshold
Prevotella corporis	strain=DSM 18810	GCA_000430525.1	28128	28128	type	True	79.7712	61	876	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	79.7332	121	876	95	below_threshold
Prevotella salivae	strain=DSM 15606	GCA_000185845.1	228604	228604	type	True	79.2481	167	876	95	below_threshold
Prevotella corporis	strain=JCM 8529	GCA_000613365.1	28128	28128	type	True	79.2413	62	876	95	below_threshold
Prevotella jejuni	strain=DSM 26989	GCA_900187995.1	1177574	1177574	type	True	79.1298	67	876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:44,200] [INFO] DFAST Taxonomy check result was written to GCF_000613785.1_ASM61378v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:44,200] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:44,200] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:44,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf0d9cd6-d820-4475-a85f-aedea444843d/dqc_reference/checkm_data
[2024-01-24 13:37:44,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:44,237] [INFO] Task started: CheckM
[2024-01-24 13:37:44,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613785.1_ASM61378v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613785.1_ASM61378v1_genomic.fna/checkm_input GCF_000613785.1_ASM61378v1_genomic.fna/checkm_result
[2024-01-24 13:38:36,437] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:36,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:36,460] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:36,460] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:36,461] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613785.1_ASM61378v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:36,461] [INFO] Task started: Blastn
[2024-01-24 13:38:36,461] [INFO] Running command: blastn -query GCF_000613785.1_ASM61378v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf0d9cd6-d820-4475-a85f-aedea444843d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613785.1_ASM61378v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:37,326] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:37,330] [INFO] Selected 21 target genomes.
[2024-01-24 13:38:37,331] [INFO] Target genome list was writen to GCF_000613785.1_ASM61378v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:37,371] [INFO] Task started: fastANI
[2024-01-24 13:38:37,371] [INFO] Running command: fastANI --query /var/lib/cwl/stge3f0407a-0802-4f17-9c40-340daf26243d/GCF_000613785.1_ASM61378v1_genomic.fna.gz --refList GCF_000613785.1_ASM61378v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613785.1_ASM61378v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:47,915] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:47,924] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:47,925] [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_000613785.1	s__Prevotella oulorum	100.0	872	876	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.00	96.91	0.92	0.84	5	conclusive
GCF_000599605.1	s__Prevotella sp000599605	91.917	689	876	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.66	96.63	0.93	0.92	3	-
GCF_000614205.1	s__Prevotella saccharolytica	82.2924	75	876	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.70	0.90	0.88	3	-
GCF_900637655.1	s__Prevotella oris	80.5909	202	876	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.96	97.06	0.90	0.82	10	-
GCF_000614025.1	s__Prevotella aurantiaca	80.3735	68	876	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.47	98.39	0.93	0.91	4	-
GCF_000382385.1	s__Prevotella maculosa	80.259	200	876	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.13	97.00	0.93	0.87	4	-
GCF_000430525.1	s__Prevotella corporis	79.7866	60	876	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.63	97.78	0.92	0.87	4	-
GCF_000185845.1	s__Prevotella salivae	79.2387	167	876	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.60	96.70	0.94	0.87	27	-
GCA_900199655.1	s__Prevotella sp900199655	78.159	84	876	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.91	99.91	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:47,926] [INFO] GTDB search result was written to GCF_000613785.1_ASM61378v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:47,927] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:47,932] [INFO] DFAST_QC result json was written to GCF_000613785.1_ASM61378v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:47,933] [INFO] DFAST_QC completed!
[2024-01-24 13:38:47,933] [INFO] Total running time: 0h1m34s