[2024-01-24 13:55:19,372] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,374] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,374] [INFO] DQC Reference Directory: /var/lib/cwl/stgd050587e-3ce8-495a-b7bc-471cddbba9a2/dqc_reference
[2024-01-24 13:55:20,793] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:20,795] [INFO] Task started: Prodigal
[2024-01-24 13:55:20,795] [INFO] Running command: gunzip -c /var/lib/cwl/stg8cef47ce-3378-4bef-834b-33f4ef4bdeb4/GCF_020179495.1_ASM2017949v1_genomic.fna.gz | prodigal -d GCF_020179495.1_ASM2017949v1_genomic.fna/cds.fna -a GCF_020179495.1_ASM2017949v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:50,593] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:50,593] [INFO] Task started: HMMsearch
[2024-01-24 13:55:50,593] [INFO] Running command: hmmsearch --tblout GCF_020179495.1_ASM2017949v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd050587e-3ce8-495a-b7bc-471cddbba9a2/dqc_reference/reference_markers.hmm GCF_020179495.1_ASM2017949v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:50,965] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:50,967] [INFO] Found 6/6 markers.
[2024-01-24 13:55:51,021] [INFO] Query marker FASTA was written to GCF_020179495.1_ASM2017949v1_genomic.fna/markers.fasta
[2024-01-24 13:55:51,022] [INFO] Task started: Blastn
[2024-01-24 13:55:51,022] [INFO] Running command: blastn -query GCF_020179495.1_ASM2017949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd050587e-3ce8-495a-b7bc-471cddbba9a2/dqc_reference/reference_markers.fasta -out GCF_020179495.1_ASM2017949v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:51,644] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:51,651] [INFO] Selected 11 target genomes.
[2024-01-24 13:55:51,652] [INFO] Target genome list was writen to GCF_020179495.1_ASM2017949v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:51,665] [INFO] Task started: fastANI
[2024-01-24 13:55:51,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cef47ce-3378-4bef-834b-33f4ef4bdeb4/GCF_020179495.1_ASM2017949v1_genomic.fna.gz --refList GCF_020179495.1_ASM2017949v1_genomic.fna/target_genomes.txt --output GCF_020179495.1_ASM2017949v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:06,599] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:06,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd050587e-3ce8-495a-b7bc-471cddbba9a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:06,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd050587e-3ce8-495a-b7bc-471cddbba9a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:06,619] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:56:06,620] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:06,620] [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 thetaiotaomicron	strain=VPI-5482	GCA_020179495.1	818	818	type	True	100.0	2044	2045	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_002959695.1	818	818	type	True	99.995	2044	2045	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	99.9934	2043	2045	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_000011065.1	818	818	type	True	99.9874	2039	2045	95	conclusive
Bacteroides thetaiotaomicron	strain=NCTC10582	GCA_900445595.1	818	818	type	True	99.9864	2018	2045	95	conclusive
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	82.3395	744	2045	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	81.8739	806	2045	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	81.8033	933	2045	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	81.758	940	2045	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.2803	336	2045	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	78.3587	394	2045	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:06,622] [INFO] DFAST Taxonomy check result was written to GCF_020179495.1_ASM2017949v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:06,623] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:06,623] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:06,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd050587e-3ce8-495a-b7bc-471cddbba9a2/dqc_reference/checkm_data
[2024-01-24 13:56:06,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:06,682] [INFO] Task started: CheckM
[2024-01-24 13:56:06,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020179495.1_ASM2017949v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020179495.1_ASM2017949v1_genomic.fna/checkm_input GCF_020179495.1_ASM2017949v1_genomic.fna/checkm_result
[2024-01-24 13:57:28,147] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:28,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:28,169] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:28,169] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:28,170] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020179495.1_ASM2017949v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:28,170] [INFO] Task started: Blastn
[2024-01-24 13:57:28,170] [INFO] Running command: blastn -query GCF_020179495.1_ASM2017949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd050587e-3ce8-495a-b7bc-471cddbba9a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_020179495.1_ASM2017949v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:29,098] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:29,101] [INFO] Selected 16 target genomes.
[2024-01-24 13:57:29,101] [INFO] Target genome list was writen to GCF_020179495.1_ASM2017949v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:29,110] [INFO] Task started: fastANI
[2024-01-24 13:57:29,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cef47ce-3378-4bef-834b-33f4ef4bdeb4/GCF_020179495.1_ASM2017949v1_genomic.fna.gz --refList GCF_020179495.1_ASM2017949v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020179495.1_ASM2017949v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:48,375] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:48,389] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:48,389] [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_000011065.1	s__Bacteroides thetaiotaomicron	99.9874	2039	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	conclusive
GCF_900106755.1	s__Bacteroides faecis	89.2952	1416	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
GCA_900755095.1	s__Bacteroides sp900755095	88.4858	690	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761785.1	s__Bacteroides sp900761785	85.0211	995	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000210075.1	s__Bacteroides xylanisolvens	82.7082	964	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCF_000156195.1	s__Bacteroides finegoldii	82.2077	764	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	98.84	97.86	0.83	0.75	21	-
GCF_900130125.1	s__Bacteroides congonensis	82.101	936	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.81	97.60	0.79	0.75	6	-
GCF_009193295.2	s__Bacteroides luhongzhouii	81.9862	907	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_012113595.1	s__Bacteroides sp012113595	81.871	966	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222615.2	s__Bacteroides caccae	81.8532	812	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.30	98.91	0.88	0.81	77	-
GCF_001314995.1	s__Bacteroides ovatus	81.7582	949	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	81.7121	950	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCF_014750685.1	s__Bacteroides sp014750685	81.6077	984	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902362375.1	s__Bacteroides sp902362375	81.5779	937	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCF_009193325.2	s__Bacteroides zhangwenhongi	81.4836	767	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	97.65	96.82	0.72	0.66	9	-
GCA_900556625.1	s__Bacteroides sp900556625	81.0945	483	2045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.84	99.84	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:48,391] [INFO] GTDB search result was written to GCF_020179495.1_ASM2017949v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:48,400] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:48,410] [INFO] DFAST_QC result json was written to GCF_020179495.1_ASM2017949v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:48,411] [INFO] DFAST_QC completed!
[2024-01-24 13:57:48,411] [INFO] Total running time: 0h2m29s