[2024-01-25 20:27:35,675] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:35,677] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:35,677] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb876189-b154-47be-9c6c-f72f7928d52b/dqc_reference
[2024-01-25 20:27:36,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:36,833] [INFO] Task started: Prodigal
[2024-01-25 20:27:36,833] [INFO] Running command: gunzip -c /var/lib/cwl/stgb49872ee-a4c4-4c64-a79d-6f672560789a/GCF_000613365.1_ASM61336v1_genomic.fna.gz | prodigal -d GCF_000613365.1_ASM61336v1_genomic.fna/cds.fna -a GCF_000613365.1_ASM61336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:48,920] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:48,920] [INFO] Task started: HMMsearch
[2024-01-25 20:27:48,920] [INFO] Running command: hmmsearch --tblout GCF_000613365.1_ASM61336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb876189-b154-47be-9c6c-f72f7928d52b/dqc_reference/reference_markers.hmm GCF_000613365.1_ASM61336v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:49,160] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:49,161] [INFO] Found 6/6 markers.
[2024-01-25 20:27:49,187] [INFO] Query marker FASTA was written to GCF_000613365.1_ASM61336v1_genomic.fna/markers.fasta
[2024-01-25 20:27:49,187] [INFO] Task started: Blastn
[2024-01-25 20:27:49,187] [INFO] Running command: blastn -query GCF_000613365.1_ASM61336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb876189-b154-47be-9c6c-f72f7928d52b/dqc_reference/reference_markers.fasta -out GCF_000613365.1_ASM61336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:49,748] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:49,751] [INFO] Selected 14 target genomes.
[2024-01-25 20:27:49,751] [INFO] Target genome list was writen to GCF_000613365.1_ASM61336v1_genomic.fna/target_genomes.txt
[2024-01-25 20:27:49,769] [INFO] Task started: fastANI
[2024-01-25 20:27:49,769] [INFO] Running command: fastANI --query /var/lib/cwl/stgb49872ee-a4c4-4c64-a79d-6f672560789a/GCF_000613365.1_ASM61336v1_genomic.fna.gz --refList GCF_000613365.1_ASM61336v1_genomic.fna/target_genomes.txt --output GCF_000613365.1_ASM61336v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:27:57,235] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:57,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb876189-b154-47be-9c6c-f72f7928d52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:27:57,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb876189-b154-47be-9c6c-f72f7928d52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:27:57,244] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:27:57,244] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:27:57,244] [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
Prevotella corporis	strain=JCM 8529	GCA_000613365.1	28128	28128	type	True	100.0	844	851	95	conclusive
Prevotella corporis	strain=DSM 18810	GCA_000430525.1	28128	28128	type	True	99.9185	844	851	95	conclusive
Prevotella colorans	strain=DSM 100333	GCA_003096815.1	1703337	1703337	type	True	85.096	102	851	95	below_threshold
Prevotella brunnea	strain=A2672	GCA_008016795.1	2508867	2508867	type	True	84.9609	335	851	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	80.6006	128	851	95	below_threshold
Prevotella scopos	strain=W2052	GCA_018127785.1	589437	589437	type	True	80.4217	127	851	95	below_threshold
Prevotella scopos	strain=DSM 22613	GCA_900129535.1	589437	589437	type	True	80.3421	122	851	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	80.0443	51	851	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	79.9809	103	851	95	below_threshold
Prevotella jejuni	strain=DSM 26989	GCA_900187995.1	1177574	1177574	type	True	79.5551	108	851	95	below_threshold
Prevotella intermedia	strain=DSM 20706	GCA_000439065.1	28131	28131	type	True	79.1777	165	851	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	79.1402	168	851	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:27:57,246] [INFO] DFAST Taxonomy check result was written to GCF_000613365.1_ASM61336v1_genomic.fna/tc_result.tsv
[2024-01-25 20:27:57,246] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:27:57,246] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:27:57,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb876189-b154-47be-9c6c-f72f7928d52b/dqc_reference/checkm_data
[2024-01-25 20:27:57,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:27:57,275] [INFO] Task started: CheckM
[2024-01-25 20:27:57,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613365.1_ASM61336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613365.1_ASM61336v1_genomic.fna/checkm_input GCF_000613365.1_ASM61336v1_genomic.fna/checkm_result
[2024-01-25 20:28:34,438] [INFO] Task succeeded: CheckM
[2024-01-25 20:28:34,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:28:34,453] [INFO] ===== Completeness check finished =====
[2024-01-25 20:28:34,454] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:28:34,458] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613365.1_ASM61336v1_genomic.fna/markers.fasta)
[2024-01-25 20:28:34,458] [INFO] Task started: Blastn
[2024-01-25 20:28:34,458] [INFO] Running command: blastn -query GCF_000613365.1_ASM61336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb876189-b154-47be-9c6c-f72f7928d52b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613365.1_ASM61336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:35,237] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:35,242] [INFO] Selected 25 target genomes.
[2024-01-25 20:28:35,242] [INFO] Target genome list was writen to GCF_000613365.1_ASM61336v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:28:35,299] [INFO] Task started: fastANI
[2024-01-25 20:28:35,299] [INFO] Running command: fastANI --query /var/lib/cwl/stgb49872ee-a4c4-4c64-a79d-6f672560789a/GCF_000613365.1_ASM61336v1_genomic.fna.gz --refList GCF_000613365.1_ASM61336v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613365.1_ASM61336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:28:47,706] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:47,716] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:28:47,716] [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_000430525.1	s__Prevotella corporis	99.9185	844	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.63	97.78	0.92	0.87	4	conclusive
GCF_008016795.1	s__Prevotella brunnea	84.9173	337	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.23	99.23	0.96	0.96	2	-
GCF_003043945.1	s__Prevotella sp003043945	81.3601	85	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.81	99.81	0.99	0.99	2	-
GCF_018127785.1	s__Prevotella scopos	80.4505	126	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	4	-
GCF_000257925.1	s__Prevotella sp000257925	80.3545	108	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.40	96.99	0.92	0.83	10	-
GCF_000377625.1	s__Prevotella veroralis	80.3284	108	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.76	96.65	0.91	0.86	4	-
GCF_900187995.1	s__Prevotella jejuni	79.5875	106	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.57	0.92	0.88	7	-
GCF_000614025.1	s__Prevotella aurantiaca	79.4865	142	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.47	98.39	0.93	0.91	4	-
GCF_001953955.1	s__Prevotella intermedia	79.2463	171	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.13	0.88	0.83	34	-
GCF_000688375.1	s__Prevotella sp000688375	78.8644	202	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613945.1	s__Prevotella falsenii	78.8363	146	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609775.1	s__Prevotella melaninogenica_A	78.4607	93	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905236755.1	s__Prevotella sp905236755	77.0624	57	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	97.34	0.84	0.68	4	-
GCA_900315635.1	s__Prevotella sp900315635	76.6655	62	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.69	99.39	0.92	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:28:47,718] [INFO] GTDB search result was written to GCF_000613365.1_ASM61336v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:28:47,718] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:28:47,721] [INFO] DFAST_QC result json was written to GCF_000613365.1_ASM61336v1_genomic.fna/dqc_result.json
[2024-01-25 20:28:47,722] [INFO] DFAST_QC completed!
[2024-01-25 20:28:47,722] [INFO] Total running time: 0h1m12s