[2024-01-25 18:41:50,835] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:41:50,837] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:41:50,837] [INFO] DQC Reference Directory: /var/lib/cwl/stg73c3af05-0665-4777-93d3-1c50bf52ddb9/dqc_reference
[2024-01-25 18:41:51,928] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:41:51,930] [INFO] Task started: Prodigal
[2024-01-25 18:41:51,930] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ea0417a-99e4-445e-9f24-d1c9b08562ec/GCF_000768685.1_ASM76868v1_genomic.fna.gz | prodigal -d GCF_000768685.1_ASM76868v1_genomic.fna/cds.fna -a GCF_000768685.1_ASM76868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:01,541] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:01,541] [INFO] Task started: HMMsearch
[2024-01-25 18:42:01,541] [INFO] Running command: hmmsearch --tblout GCF_000768685.1_ASM76868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73c3af05-0665-4777-93d3-1c50bf52ddb9/dqc_reference/reference_markers.hmm GCF_000768685.1_ASM76868v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:01,738] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:01,739] [INFO] Found 6/6 markers.
[2024-01-25 18:42:01,767] [INFO] Query marker FASTA was written to GCF_000768685.1_ASM76868v1_genomic.fna/markers.fasta
[2024-01-25 18:42:01,767] [INFO] Task started: Blastn
[2024-01-25 18:42:01,767] [INFO] Running command: blastn -query GCF_000768685.1_ASM76868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73c3af05-0665-4777-93d3-1c50bf52ddb9/dqc_reference/reference_markers.fasta -out GCF_000768685.1_ASM76868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:02,903] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:02,906] [INFO] Selected 17 target genomes.
[2024-01-25 18:42:02,906] [INFO] Target genome list was writen to GCF_000768685.1_ASM76868v1_genomic.fna/target_genomes.txt
[2024-01-25 18:42:02,912] [INFO] Task started: fastANI
[2024-01-25 18:42:02,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea0417a-99e4-445e-9f24-d1c9b08562ec/GCF_000768685.1_ASM76868v1_genomic.fna.gz --refList GCF_000768685.1_ASM76868v1_genomic.fna/target_genomes.txt --output GCF_000768685.1_ASM76868v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:16,489] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:16,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73c3af05-0665-4777-93d3-1c50bf52ddb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:16,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73c3af05-0665-4777-93d3-1c50bf52ddb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:16,500] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:42:16,500] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:42:16,500] [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
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	100.0	1172	1173	95	conclusive
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	84.572	821	1173	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	84.5496	840	1173	95	below_threshold
Knoellia sinensis	strain=KCTC 19936	GCA_000768705.1	136100	136100	type	True	83.9494	842	1173	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	83.4079	756	1173	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	83.3957	755	1173	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	80.5835	586	1173	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	80.4317	576	1173	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	80.0801	505	1173	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.8961	426	1173	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	79.8774	528	1173	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	79.5546	495	1173	95	below_threshold
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	79.5366	485	1173	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	79.4892	478	1173	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.8531	378	1173	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.6146	332	1173	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.5824	376	1173	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:16,503] [INFO] DFAST Taxonomy check result was written to GCF_000768685.1_ASM76868v1_genomic.fna/tc_result.tsv
[2024-01-25 18:42:16,504] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:16,504] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:16,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73c3af05-0665-4777-93d3-1c50bf52ddb9/dqc_reference/checkm_data
[2024-01-25 18:42:16,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:16,541] [INFO] Task started: CheckM
[2024-01-25 18:42:16,542] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000768685.1_ASM76868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000768685.1_ASM76868v1_genomic.fna/checkm_input GCF_000768685.1_ASM76868v1_genomic.fna/checkm_result
[2024-01-25 18:43:17,668] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:17,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:17,685] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:17,686] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:17,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000768685.1_ASM76868v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:17,687] [INFO] Task started: Blastn
[2024-01-25 18:43:17,687] [INFO] Running command: blastn -query GCF_000768685.1_ASM76868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73c3af05-0665-4777-93d3-1c50bf52ddb9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000768685.1_ASM76868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:19,561] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:19,564] [INFO] Selected 10 target genomes.
[2024-01-25 18:43:19,564] [INFO] Target genome list was writen to GCF_000768685.1_ASM76868v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:19,576] [INFO] Task started: fastANI
[2024-01-25 18:43:19,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea0417a-99e4-445e-9f24-d1c9b08562ec/GCF_000768685.1_ASM76868v1_genomic.fna.gz --refList GCF_000768685.1_ASM76868v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000768685.1_ASM76868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:29,160] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:29,167] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:29,168] [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_000768685.1	s__Knoellia subterranea	100.0	1172	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007992835.1	s__Knoellia locipacati	84.5855	845	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768675.1	s__Knoellia flava	84.5649	821	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000768705.1	s__Knoellia sinensis	83.9635	841	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152705.1	s__Knoellia sp000152705	83.8093	872	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427985.1	s__Knoellia sp001427985	83.6851	793	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002895.1	s__Knoellia remsis	83.4433	751	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768695.1	s__Knoellia aerolata	83.396	757	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763705.1	s__Phycicoccus sp014763705	80.3698	437	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846495.1	s__Phycicoccus duodecadis	79.8679	529	1173	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:29,169] [INFO] GTDB search result was written to GCF_000768685.1_ASM76868v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:29,169] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:29,172] [INFO] DFAST_QC result json was written to GCF_000768685.1_ASM76868v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:29,173] [INFO] DFAST_QC completed!
[2024-01-25 18:43:29,173] [INFO] Total running time: 0h1m38s