[2024-01-24 14:47:19,988] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:19,990] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:19,990] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c4309cb-287f-4c53-bfce-652b8aa6fb96/dqc_reference
[2024-01-24 14:47:21,212] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:21,213] [INFO] Task started: Prodigal
[2024-01-24 14:47:21,214] [INFO] Running command: gunzip -c /var/lib/cwl/stgd174d821-eaf8-416b-a7f6-4238e21607ad/GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/cds.fna -a GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:40,639] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:40,640] [INFO] Task started: HMMsearch
[2024-01-24 14:47:40,640] [INFO] Running command: hmmsearch --tblout GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c4309cb-287f-4c53-bfce-652b8aa6fb96/dqc_reference/reference_markers.hmm GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:40,950] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:40,952] [INFO] Found 6/6 markers.
[2024-01-24 14:47:40,989] [INFO] Query marker FASTA was written to GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:47:40,990] [INFO] Task started: Blastn
[2024-01-24 14:47:40,990] [INFO] Running command: blastn -query GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c4309cb-287f-4c53-bfce-652b8aa6fb96/dqc_reference/reference_markers.fasta -out GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:41,669] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:41,674] [INFO] Selected 13 target genomes.
[2024-01-24 14:47:41,674] [INFO] Target genome list was writen to GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:47:41,701] [INFO] Task started: fastANI
[2024-01-24 14:47:41,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgd174d821-eaf8-416b-a7f6-4238e21607ad/GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna.gz --refList GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:54,129] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:54,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c4309cb-287f-4c53-bfce-652b8aa6fb96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:54,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c4309cb-287f-4c53-bfce-652b8aa6fb96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:54,145] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:54,145] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:54,146] [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 clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	100.0	1240	1241	95	conclusive
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	99.9915	1233	1241	95	conclusive
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	87.5299	839	1241	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	87.5008	844	1241	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	87.4528	832	1241	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	85.0939	796	1241	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	85.0859	800	1241	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	85.062	800	1241	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	84.0531	813	1241	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	84.0434	796	1241	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	80.2963	529	1241	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	80.2465	547	1241	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:54,152] [INFO] DFAST Taxonomy check result was written to GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:47:54,153] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:54,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:54,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c4309cb-287f-4c53-bfce-652b8aa6fb96/dqc_reference/checkm_data
[2024-01-24 14:47:54,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:54,206] [INFO] Task started: CheckM
[2024-01-24 14:47:54,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/checkm_input GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:48:54,031] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:54,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:54,051] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:54,051] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:54,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:48:54,052] [INFO] Task started: Blastn
[2024-01-24 14:48:54,052] [INFO] Running command: blastn -query GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c4309cb-287f-4c53-bfce-652b8aa6fb96/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:54,997] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:55,000] [INFO] Selected 9 target genomes.
[2024-01-24 14:48:55,001] [INFO] Target genome list was writen to GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:55,021] [INFO] Task started: fastANI
[2024-01-24 14:48:55,021] [INFO] Running command: fastANI --query /var/lib/cwl/stgd174d821-eaf8-416b-a7f6-4238e21607ad/GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna.gz --refList GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:03,120] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:03,128] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:03,128] [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_900129655.1	s__Bacteroides clarus	100.0	1240	1241	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	conclusive
GCF_000154525.1	s__Bacteroides stercoris	87.5143	840	1241	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_003438615.1	s__Bacteroides sp003545565	87.4831	837	1241	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_000155815.1	s__Bacteroides eggerthii	85.104	795	1241	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	-
GCF_000374365.1	s__Bacteroides gallinarum	84.0599	812	1241	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCA_910578895.1	s__Bacteroides sp910578895	83.8164	658	1241	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195635.1	s__Bacteroides fluxus	80.2327	527	1241	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCF_014750685.1	s__Bacteroides sp014750685	78.4421	294	1241	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:03,132] [INFO] GTDB search result was written to GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:03,133] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:03,136] [INFO] DFAST_QC result json was written to GCF_900129655.1_IMG-taxon_2695420967_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:49:03,136] [INFO] DFAST_QC completed!
[2024-01-24 14:49:03,136] [INFO] Total running time: 0h1m43s