[2024-01-25 17:50:20,445] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:50:20,447] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:50:20,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg515ada11-25e4-488b-a104-c099f0a2d03f/dqc_reference
[2024-01-25 17:50:21,631] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:50:21,631] [INFO] Task started: Prodigal
[2024-01-25 17:50:21,631] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc28564b-d86d-4111-9312-5fb1c58acb6a/GCF_000210075.1_ASM21007v1_genomic.fna.gz | prodigal -d GCF_000210075.1_ASM21007v1_genomic.fna/cds.fna -a GCF_000210075.1_ASM21007v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:45,580] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:45,581] [INFO] Task started: HMMsearch
[2024-01-25 17:50:45,581] [INFO] Running command: hmmsearch --tblout GCF_000210075.1_ASM21007v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg515ada11-25e4-488b-a104-c099f0a2d03f/dqc_reference/reference_markers.hmm GCF_000210075.1_ASM21007v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:45,843] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:45,844] [INFO] Found 6/6 markers.
[2024-01-25 17:50:45,889] [INFO] Query marker FASTA was written to GCF_000210075.1_ASM21007v1_genomic.fna/markers.fasta
[2024-01-25 17:50:45,889] [INFO] Task started: Blastn
[2024-01-25 17:50:45,889] [INFO] Running command: blastn -query GCF_000210075.1_ASM21007v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg515ada11-25e4-488b-a104-c099f0a2d03f/dqc_reference/reference_markers.fasta -out GCF_000210075.1_ASM21007v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:46,464] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:46,468] [INFO] Selected 16 target genomes.
[2024-01-25 17:50:46,468] [INFO] Target genome list was writen to GCF_000210075.1_ASM21007v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:46,521] [INFO] Task started: fastANI
[2024-01-25 17:50:46,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc28564b-d86d-4111-9312-5fb1c58acb6a/GCF_000210075.1_ASM21007v1_genomic.fna.gz --refList GCF_000210075.1_ASM21007v1_genomic.fna/target_genomes.txt --output GCF_000210075.1_ASM21007v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:05,427] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:05,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg515ada11-25e4-488b-a104-c099f0a2d03f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:05,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg515ada11-25e4-488b-a104-c099f0a2d03f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:05,436] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:51:05,436] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:05,436] [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 xylanisolvens	strain=XB1A	GCA_000210075.1	371601	371601	suspected-type	True	99.9993	1984	1992	95	conclusive
Bacteroides luhongzhouii	strain=HF-5141	GCA_009193295.2	2650158	2650158	type	True	93.9765	1334	1992	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	92.805	1410	1992	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_001314995.1	28116	28116	suspected-type	True	92.7828	1412	1992	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	92.7529	1416	1992	95	below_threshold
Bacteroides ovatus	strain=NCTC11153	GCA_900445505.1	28116	28116	suspected-type	True	92.7065	1422	1992	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_002959635.1	28116	28116	suspected-type	True	92.6971	1422	1992	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	92.5953	1011	1992	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	92.4189	1010	1992	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_001688725.2	1796613	1796613	type	True	92.3944	1024	1992	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	92.3859	1025	1992	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	83.1539	852	1992	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	82.7574	972	1992	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:05,438] [INFO] DFAST Taxonomy check result was written to GCF_000210075.1_ASM21007v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:05,438] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:05,438] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:05,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg515ada11-25e4-488b-a104-c099f0a2d03f/dqc_reference/checkm_data
[2024-01-25 17:51:05,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:05,493] [INFO] Task started: CheckM
[2024-01-25 17:51:05,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000210075.1_ASM21007v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000210075.1_ASM21007v1_genomic.fna/checkm_input GCF_000210075.1_ASM21007v1_genomic.fna/checkm_result
[2024-01-25 17:52:09,503] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:09,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:09,523] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:09,524] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:09,525] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000210075.1_ASM21007v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:09,525] [INFO] Task started: Blastn
[2024-01-25 17:52:09,525] [INFO] Running command: blastn -query GCF_000210075.1_ASM21007v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg515ada11-25e4-488b-a104-c099f0a2d03f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000210075.1_ASM21007v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:10,404] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:10,407] [INFO] Selected 10 target genomes.
[2024-01-25 17:52:10,407] [INFO] Target genome list was writen to GCF_000210075.1_ASM21007v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:10,418] [INFO] Task started: fastANI
[2024-01-25 17:52:10,418] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc28564b-d86d-4111-9312-5fb1c58acb6a/GCF_000210075.1_ASM21007v1_genomic.fna.gz --refList GCF_000210075.1_ASM21007v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000210075.1_ASM21007v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:23,333] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:23,341] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:23,341] [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_000210075.1	s__Bacteroides xylanisolvens	99.9993	1984	1992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	conclusive
GCF_009193295.2	s__Bacteroides luhongzhouii	93.9695	1334	1992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_001314995.1	s__Bacteroides ovatus	92.7834	1411	1992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCF_001688725.2	s__Bacteroides caecimuris	92.3635	1026	1992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	90.2837	1425	1992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCA_902362375.1	s__Bacteroides sp902362375	89.695	1283	1992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCA_900755095.1	s__Bacteroides sp900755095	89.4881	626	1992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156195.1	s__Bacteroides finegoldii	85.5724	912	1992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	98.84	97.86	0.83	0.75	21	-
GCF_009193325.2	s__Bacteroides zhangwenhongi	84.3825	970	1992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	97.65	96.82	0.72	0.66	9	-
GCF_900106755.1	s__Bacteroides faecis	81.8679	875	1992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:23,342] [INFO] GTDB search result was written to GCF_000210075.1_ASM21007v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:23,343] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:23,346] [INFO] DFAST_QC result json was written to GCF_000210075.1_ASM21007v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:23,346] [INFO] DFAST_QC completed!
[2024-01-25 17:52:23,346] [INFO] Total running time: 0h2m3s