[2024-01-24 13:17:13,768] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,770] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,771] [INFO] DQC Reference Directory: /var/lib/cwl/stg281e6557-99fc-4089-8f20-355cf31d66d1/dqc_reference
[2024-01-24 13:17:15,104] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,105] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg680df7f3-a1f7-4822-a9d4-d74a34a6d2c5/GCF_022453665.1_ASM2245366v1_genomic.fna.gz | prodigal -d GCF_022453665.1_ASM2245366v1_genomic.fna/cds.fna -a GCF_022453665.1_ASM2245366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:45,174] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:45,174] [INFO] Task started: HMMsearch
[2024-01-24 13:17:45,175] [INFO] Running command: hmmsearch --tblout GCF_022453665.1_ASM2245366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg281e6557-99fc-4089-8f20-355cf31d66d1/dqc_reference/reference_markers.hmm GCF_022453665.1_ASM2245366v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:45,538] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:45,540] [INFO] Found 6/6 markers.
[2024-01-24 13:17:45,599] [INFO] Query marker FASTA was written to GCF_022453665.1_ASM2245366v1_genomic.fna/markers.fasta
[2024-01-24 13:17:45,600] [INFO] Task started: Blastn
[2024-01-24 13:17:45,600] [INFO] Running command: blastn -query GCF_022453665.1_ASM2245366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg281e6557-99fc-4089-8f20-355cf31d66d1/dqc_reference/reference_markers.fasta -out GCF_022453665.1_ASM2245366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:46,261] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:46,266] [INFO] Selected 11 target genomes.
[2024-01-24 13:17:46,266] [INFO] Target genome list was writen to GCF_022453665.1_ASM2245366v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:46,271] [INFO] Task started: fastANI
[2024-01-24 13:17:46,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg680df7f3-a1f7-4822-a9d4-d74a34a6d2c5/GCF_022453665.1_ASM2245366v1_genomic.fna.gz --refList GCF_022453665.1_ASM2245366v1_genomic.fna/target_genomes.txt --output GCF_022453665.1_ASM2245366v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:02,010] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:02,011] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg281e6557-99fc-4089-8f20-355cf31d66d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:02,012] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg281e6557-99fc-4089-8f20-355cf31d66d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:02,028] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:18:02,028] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:02,029] [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_022453665.1	818	818	type	True	100.0	2102	2104	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_002959695.1	818	818	type	True	99.9953	2098	2104	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_000011065.1	818	818	type	True	99.9921	2093	2104	95	conclusive
Bacteroides thetaiotaomicron	strain=NCTC10582	GCA_900445595.1	818	818	type	True	99.9848	2072	2104	95	conclusive
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_020179495.1	818	818	type	True	99.9763	2041	2104	95	conclusive
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	82.4523	748	2104	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	82.1477	810	2104	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	81.9831	951	2104	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	81.9132	954	2104	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.5012	338	2104	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	78.4214	401	2104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:02,031] [INFO] DFAST Taxonomy check result was written to GCF_022453665.1_ASM2245366v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:02,032] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:02,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:02,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg281e6557-99fc-4089-8f20-355cf31d66d1/dqc_reference/checkm_data
[2024-01-24 13:18:02,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:02,106] [INFO] Task started: CheckM
[2024-01-24 13:18:02,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022453665.1_ASM2245366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022453665.1_ASM2245366v1_genomic.fna/checkm_input GCF_022453665.1_ASM2245366v1_genomic.fna/checkm_result
[2024-01-24 13:19:26,262] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:26,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:26,305] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:26,305] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:26,305] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022453665.1_ASM2245366v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:26,306] [INFO] Task started: Blastn
[2024-01-24 13:19:26,306] [INFO] Running command: blastn -query GCF_022453665.1_ASM2245366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg281e6557-99fc-4089-8f20-355cf31d66d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_022453665.1_ASM2245366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:27,220] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:27,224] [INFO] Selected 16 target genomes.
[2024-01-24 13:19:27,224] [INFO] Target genome list was writen to GCF_022453665.1_ASM2245366v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:27,239] [INFO] Task started: fastANI
[2024-01-24 13:19:27,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg680df7f3-a1f7-4822-a9d4-d74a34a6d2c5/GCF_022453665.1_ASM2245366v1_genomic.fna.gz --refList GCF_022453665.1_ASM2245366v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022453665.1_ASM2245366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:47,258] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:47,271] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:47,272] [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	99.9917	2093	2104	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	89.2748	1420	2104	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	88.8734	668	2104	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	85.0031	1006	2104	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	82.8787	964	2104	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	82.2213	784	2104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	98.84	97.86	0.83	0.75	21	-
GCF_002222615.2	s__Bacteroides caccae	82.1906	809	2104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.30	98.91	0.88	0.81	77	-
GCF_009193295.2	s__Bacteroides luhongzhouii	82.1517	911	2104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_900130125.1	s__Bacteroides congonensis	82.0931	960	2104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.81	97.60	0.79	0.75	6	-
GCF_001314995.1	s__Bacteroides ovatus	81.9744	954	2104	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	81.879	955	2104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCF_012113595.1	s__Bacteroides sp012113595	81.864	978	2104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014750685.1	s__Bacteroides sp014750685	81.6479	981	2104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193325.2	s__Bacteroides zhangwenhongi	81.4766	792	2104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	97.65	96.82	0.72	0.66	9	-
GCA_902362375.1	s__Bacteroides sp902362375	81.4302	959	2104	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCA_900556625.1	s__Bacteroides sp900556625	80.9795	478	2104	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 13:19:47,274] [INFO] GTDB search result was written to GCF_022453665.1_ASM2245366v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:47,275] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:47,280] [INFO] DFAST_QC result json was written to GCF_022453665.1_ASM2245366v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:47,281] [INFO] DFAST_QC completed!
[2024-01-24 13:19:47,281] [INFO] Total running time: 0h2m34s