[2024-01-24 14:07:15,027] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:15,028] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:15,029] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3526d4d-baa7-4478-84fc-2171a7f32d9b/dqc_reference
[2024-01-24 14:07:16,438] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:16,439] [INFO] Task started: Prodigal
[2024-01-24 14:07:16,439] [INFO] Running command: gunzip -c /var/lib/cwl/stg312f8805-9b6e-4dac-b222-b4c12abded9d/GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/cds.fna -a GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:28,313] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:28,314] [INFO] Task started: HMMsearch
[2024-01-24 14:07:28,314] [INFO] Running command: hmmsearch --tblout GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3526d4d-baa7-4478-84fc-2171a7f32d9b/dqc_reference/reference_markers.hmm GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:28,585] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:28,587] [INFO] Found 6/6 markers.
[2024-01-24 14:07:28,623] [INFO] Query marker FASTA was written to GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:07:28,624] [INFO] Task started: Blastn
[2024-01-24 14:07:28,624] [INFO] Running command: blastn -query GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3526d4d-baa7-4478-84fc-2171a7f32d9b/dqc_reference/reference_markers.fasta -out GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:29,588] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:29,593] [INFO] Selected 13 target genomes.
[2024-01-24 14:07:29,593] [INFO] Target genome list was writen to GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:07:29,605] [INFO] Task started: fastANI
[2024-01-24 14:07:29,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg312f8805-9b6e-4dac-b222-b4c12abded9d/GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna.gz --refList GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:41,047] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:41,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3526d4d-baa7-4478-84fc-2171a7f32d9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:41,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3526d4d-baa7-4478-84fc-2171a7f32d9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:41,059] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:07:41,060] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:41,060] [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
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	100.0	1229	1232	95	conclusive
Cryobacterium levicorallinum	strain=Hh34	GCA_004402405.1	995038	995038	type	True	99.9885	1220	1232	95	conclusive
Cryobacterium levicorallinum	strain=NBRC 107883	GCA_007992355.1	995038	995038	type	True	99.9544	1201	1232	95	conclusive
Cryobacterium flavum	strain=CGMCC 1.11215	GCA_900103805.1	1424659	1424659	type	True	86.0048	869	1232	95	below_threshold
Cryobacterium flavum	strain=Hh8	GCA_004402625.1	1424659	1424659	type	True	85.988	868	1232	95	below_threshold
Cryobacterium aureum	strain=Hh31	GCA_002954245.1	995037	995037	type	True	85.4353	862	1232	95	below_threshold
Cryobacterium luteum	strain=CGMCC 1.11210	GCA_900110125.1	1424661	1424661	type	True	85.3758	820	1232	95	below_threshold
Cryobacterium luteum	strain=Hh15	GCA_004402515.1	1424661	1424661	type	True	85.3506	814	1232	95	below_threshold
Cryobacterium ruanii	strain=Sr36	GCA_004404055.1	1259197	1259197	type	True	85.0126	813	1232	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	80.2141	513	1232	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.9307	315	1232	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.9134	343	1232	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	77.6476	307	1232	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:41,065] [INFO] DFAST Taxonomy check result was written to GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:07:41,065] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:41,065] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:41,066] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3526d4d-baa7-4478-84fc-2171a7f32d9b/dqc_reference/checkm_data
[2024-01-24 14:07:41,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:41,111] [INFO] Task started: CheckM
[2024-01-24 14:07:41,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/checkm_input GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:08:17,565] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:17,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:17,587] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:17,587] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:17,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:08:17,588] [INFO] Task started: Blastn
[2024-01-24 14:08:17,588] [INFO] Running command: blastn -query GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3526d4d-baa7-4478-84fc-2171a7f32d9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:19,052] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:19,056] [INFO] Selected 13 target genomes.
[2024-01-24 14:08:19,056] [INFO] Target genome list was writen to GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:19,067] [INFO] Task started: fastANI
[2024-01-24 14:08:19,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg312f8805-9b6e-4dac-b222-b4c12abded9d/GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna.gz --refList GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:31,293] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:31,307] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:31,307] [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_004402405.1	s__Cryobacterium levicorallinum	99.9885	1220	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.20	96.46	0.88	0.78	9	conclusive
GCF_002929805.1	s__Cryobacterium sp002929805	90.0919	941	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.19	99.19	0.89	0.89	2	-
GCF_900103805.1	s__Cryobacterium flavum	86.0088	868	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.64	97.38	0.89	0.83	6	-
GCF_004402535.1	s__Cryobacterium sp004402535	85.929	831	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929535.1	s__Cryobacterium sp002929535	85.4664	830	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954245.1	s__Cryobacterium aureum	85.4428	862	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110125.1	s__Cryobacterium luteum	85.3759	820	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.76	99.53	0.96	0.95	3	-
GCF_004404055.1	s__Cryobacterium ruanii	85.0126	813	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403985.1	s__Cryobacterium sp004403985	84.9339	824	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.96	97.96	0.88	0.88	2	-
GCF_004403185.1	s__Cryobacterium sp004403185	84.8327	798	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929825.1	s__Cryobacterium sp002929825	84.773	803	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	95.15	95.07	0.83	0.81	4	-
GCF_002929495.1	s__Cryobacterium sp002929495	84.7426	819	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.09	97.09	0.88	0.88	2	-
GCF_015751745.1	s__Cryobacterium sp015751745	84.713	797	1232	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:31,309] [INFO] GTDB search result was written to GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:31,310] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:31,313] [INFO] DFAST_QC result json was written to GCF_900113585.1_IMG-taxon_2663762754_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:08:31,313] [INFO] DFAST_QC completed!
[2024-01-24 14:08:31,314] [INFO] Total running time: 0h1m16s