[2024-01-24 15:11:10,054] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:11:10,056] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:11:10,056] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f183fd4-bbc3-4f10-b785-b793f6058118/dqc_reference
[2024-01-24 15:11:11,451] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:11:11,452] [INFO] Task started: Prodigal
[2024-01-24 15:11:11,452] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e8519f4-118f-447e-aa76-9524f30350f6/GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/cds.fna -a GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:45,458] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:45,459] [INFO] Task started: HMMsearch
[2024-01-24 15:11:45,459] [INFO] Running command: hmmsearch --tblout GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f183fd4-bbc3-4f10-b785-b793f6058118/dqc_reference/reference_markers.hmm GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:45,794] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:45,795] [INFO] Found 6/6 markers.
[2024-01-24 15:11:45,850] [INFO] Query marker FASTA was written to GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:11:45,850] [INFO] Task started: Blastn
[2024-01-24 15:11:45,850] [INFO] Running command: blastn -query GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f183fd4-bbc3-4f10-b785-b793f6058118/dqc_reference/reference_markers.fasta -out GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:46,452] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:46,455] [INFO] Selected 14 target genomes.
[2024-01-24 15:11:46,456] [INFO] Target genome list was writen to GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:11:46,465] [INFO] Task started: fastANI
[2024-01-24 15:11:46,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e8519f4-118f-447e-aa76-9524f30350f6/GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna.gz --refList GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:12:05,365] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:05,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f183fd4-bbc3-4f10-b785-b793f6058118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:12:05,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f183fd4-bbc3-4f10-b785-b793f6058118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:12:05,377] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:12:05,378] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:12:05,378] [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
Bacteroides stercorirosoris	strain=DSM 26884	GCA_900142015.1	871324	871324	type	True	100.0	2046	2049	95	conclusive
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	99.921	1943	2049	95	conclusive
Bacteroides oleiciplenus	strain=YIT 12058	GCA_000315485.1	626931	626931	type	True	88.287	1303	2049	95	below_threshold
Bacteroides intestinalis	strain=DSM 17393	GCA_000172175.1	329854	329854	type	True	85.6668	1175	2049	95	below_threshold
Bacteroides timonensis		GCA_000513195.1	1470345	1470345	type	True	85.4308	1215	2049	95	below_threshold
Bacteroides cellulosilyticus	strain=DSM 14838	GCA_000158035.1	246787	246787	type	True	84.328	1251	2049	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.6551	492	2049	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	80.1131	582	2049	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	80.0782	483	2049	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	79.9566	495	2049	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	79.81	569	2049	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	79.5836	483	2049	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	78.5153	394	2049	95	below_threshold
Parabacteroides goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	77.7753	139	2049	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:12:05,380] [INFO] DFAST Taxonomy check result was written to GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:12:05,380] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:12:05,380] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:12:05,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f183fd4-bbc3-4f10-b785-b793f6058118/dqc_reference/checkm_data
[2024-01-24 15:12:05,381] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:12:05,443] [INFO] Task started: CheckM
[2024-01-24 15:12:05,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/checkm_input GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:13:31,625] [INFO] Task succeeded: CheckM
[2024-01-24 15:13:31,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:13:31,649] [INFO] ===== Completeness check finished =====
[2024-01-24 15:13:31,649] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:13:31,650] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:13:31,650] [INFO] Task started: Blastn
[2024-01-24 15:13:31,650] [INFO] Running command: blastn -query GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f183fd4-bbc3-4f10-b785-b793f6058118/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:13:32,510] [INFO] Task succeeded: Blastn
[2024-01-24 15:13:32,515] [INFO] Selected 13 target genomes.
[2024-01-24 15:13:32,515] [INFO] Target genome list was writen to GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:13:32,554] [INFO] Task started: fastANI
[2024-01-24 15:13:32,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e8519f4-118f-447e-aa76-9524f30350f6/GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna.gz --refList GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:13:51,526] [INFO] Task succeeded: fastANI
[2024-01-24 15:13:51,542] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:13:51,542] [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_900142015.1	s__Bacteroides stercorirosoris	100.0	2046	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.49	98.12	0.84	0.77	7	conclusive
GCA_905215555.1	s__Bacteroides sp905215555	90.7391	1122	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315485.1	s__Bacteroides oleiciplenus	88.2872	1303	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.39	98.79	0.93	0.86	3	-
GCA_905207245.1	s__Bacteroides sp905207245	88.2011	1133	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019129285.1	s__Bacteroides sp900552405	86.5958	1346	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.09	95.34	0.92	0.76	12	-
GCF_000513195.1	s__Bacteroides timonensis	85.4324	1217	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158035.1	s__Bacteroides cellulosilyticus	84.356	1248	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.21	95.02	0.83	0.72	42	-
GCA_900557355.1	s__Bacteroides sp900557355	84.1685	653	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.57	98.57	0.54	0.54	2	-
GCF_902364365.1	s__Bacteroides sp900556215	83.666	1152	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	99.84	99.69	0.91	0.82	3	-
GCF_003464595.1	s__Bacteroides intestinalis_A	83.5029	1143	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	97.86	96.66	0.85	0.74	7	-
GCF_003438615.1	s__Bacteroides sp003545565	80.5943	517	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCA_900555635.1	s__Bacteroides sp900555635	78.5812	493	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.02	98.02	0.75	0.75	2	-
GCF_000969835.1	s__Parabacteroides goldsteinii	77.7755	139	2049	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.03	95.33	0.85	0.78	37	-
--------------------------------------------------------------------------------
[2024-01-24 15:13:51,544] [INFO] GTDB search result was written to GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:13:51,544] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:13:51,548] [INFO] DFAST_QC result json was written to GCF_900142015.1_IMG-taxon_2700988705_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:13:51,548] [INFO] DFAST_QC completed!
[2024-01-24 15:13:51,548] [INFO] Total running time: 0h2m41s