[2024-01-24 13:36:31,321] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:31,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:31,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg5266c3c1-72e4-4e6a-9c5a-740d96f23f48/dqc_reference
[2024-01-24 13:36:32,728] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:32,729] [INFO] Task started: Prodigal
[2024-01-24 13:36:32,729] [INFO] Running command: gunzip -c /var/lib/cwl/stgf34c3992-5939-4439-9b5a-84f740ddedba/GCF_009193295.2_ASM919329v2_genomic.fna.gz | prodigal -d GCF_009193295.2_ASM919329v2_genomic.fna/cds.fna -a GCF_009193295.2_ASM919329v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:00,653] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:00,654] [INFO] Task started: HMMsearch
[2024-01-24 13:37:00,654] [INFO] Running command: hmmsearch --tblout GCF_009193295.2_ASM919329v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5266c3c1-72e4-4e6a-9c5a-740d96f23f48/dqc_reference/reference_markers.hmm GCF_009193295.2_ASM919329v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:01,011] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:01,013] [INFO] Found 6/6 markers.
[2024-01-24 13:37:01,064] [INFO] Query marker FASTA was written to GCF_009193295.2_ASM919329v2_genomic.fna/markers.fasta
[2024-01-24 13:37:01,064] [INFO] Task started: Blastn
[2024-01-24 13:37:01,064] [INFO] Running command: blastn -query GCF_009193295.2_ASM919329v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5266c3c1-72e4-4e6a-9c5a-740d96f23f48/dqc_reference/reference_markers.fasta -out GCF_009193295.2_ASM919329v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:01,703] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:01,707] [INFO] Selected 12 target genomes.
[2024-01-24 13:37:01,707] [INFO] Target genome list was writen to GCF_009193295.2_ASM919329v2_genomic.fna/target_genomes.txt
[2024-01-24 13:37:01,717] [INFO] Task started: fastANI
[2024-01-24 13:37:01,718] [INFO] Running command: fastANI --query /var/lib/cwl/stgf34c3992-5939-4439-9b5a-84f740ddedba/GCF_009193295.2_ASM919329v2_genomic.fna.gz --refList GCF_009193295.2_ASM919329v2_genomic.fna/target_genomes.txt --output GCF_009193295.2_ASM919329v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:16,392] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:16,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5266c3c1-72e4-4e6a-9c5a-740d96f23f48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:16,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5266c3c1-72e4-4e6a-9c5a-740d96f23f48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:16,407] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:16,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:16,407] [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 luhongzhouii	strain=HF-5141	GCA_009193295.2	2650158	2650158	type	True	100.0	1920	1920	95	conclusive
Bacteroides xylanisolvens	strain=XB1A	GCA_000210075.1	371601	371601	suspected-type	True	94.0222	1334	1920	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_001314995.1	28116	28116	suspected-type	True	91.3849	1336	1920	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	91.3665	1330	1920	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	91.3457	951	1920	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_002959635.1	28116	28116	suspected-type	True	91.3352	1330	1920	95	below_threshold
Bacteroides ovatus	strain=NCTC11153	GCA_900445505.1	28116	28116	suspected-type	True	91.3243	1333	1920	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	91.3197	1322	1920	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	91.2905	960	1920	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	91.286	961	1920	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	83.1541	845	1920	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	82.1768	919	1920	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:16,409] [INFO] DFAST Taxonomy check result was written to GCF_009193295.2_ASM919329v2_genomic.fna/tc_result.tsv
[2024-01-24 13:37:16,410] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:16,410] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:16,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5266c3c1-72e4-4e6a-9c5a-740d96f23f48/dqc_reference/checkm_data
[2024-01-24 13:37:16,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:16,465] [INFO] Task started: CheckM
[2024-01-24 13:37:16,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009193295.2_ASM919329v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009193295.2_ASM919329v2_genomic.fna/checkm_input GCF_009193295.2_ASM919329v2_genomic.fna/checkm_result
[2024-01-24 13:38:34,899] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:34,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:34,921] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:34,922] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:34,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009193295.2_ASM919329v2_genomic.fna/markers.fasta)
[2024-01-24 13:38:34,923] [INFO] Task started: Blastn
[2024-01-24 13:38:34,923] [INFO] Running command: blastn -query GCF_009193295.2_ASM919329v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5266c3c1-72e4-4e6a-9c5a-740d96f23f48/dqc_reference/reference_markers_gtdb.fasta -out GCF_009193295.2_ASM919329v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:35,774] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:35,778] [INFO] Selected 9 target genomes.
[2024-01-24 13:38:35,778] [INFO] Target genome list was writen to GCF_009193295.2_ASM919329v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:35,798] [INFO] Task started: fastANI
[2024-01-24 13:38:35,798] [INFO] Running command: fastANI --query /var/lib/cwl/stgf34c3992-5939-4439-9b5a-84f740ddedba/GCF_009193295.2_ASM919329v2_genomic.fna.gz --refList GCF_009193295.2_ASM919329v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009193295.2_ASM919329v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:47,017] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:47,031] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:47,031] [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_009193295.2	s__Bacteroides luhongzhouii	100.0	1919	1920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	conclusive
GCF_000210075.1	s__Bacteroides xylanisolvens	94.0153	1334	1920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCF_001688725.2	s__Bacteroides caecimuris	91.4334	953	1920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCF_001314995.1	s__Bacteroides ovatus	91.3804	1337	1920	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	89.7646	1311	1920	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	89.4735	1331	1920	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	88.7262	608	1920	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	85.0656	867	1920	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	84.3232	926	1920	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	97.65	96.82	0.72	0.66	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:47,033] [INFO] GTDB search result was written to GCF_009193295.2_ASM919329v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:47,034] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:47,037] [INFO] DFAST_QC result json was written to GCF_009193295.2_ASM919329v2_genomic.fna/dqc_result.json
[2024-01-24 13:38:47,037] [INFO] DFAST_QC completed!
[2024-01-24 13:38:47,037] [INFO] Total running time: 0h2m16s