[2024-01-24 13:12:38,231] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:38,233] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:38,233] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f203c63-7289-4565-ae5d-03aa7eefd499/dqc_reference
[2024-01-24 13:12:39,615] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:39,616] [INFO] Task started: Prodigal
[2024-01-24 13:12:39,616] [INFO] Running command: gunzip -c /var/lib/cwl/stgea599bdd-f521-4bfc-be49-de9ddbf051b8/GCF_004402515.1_ASM440251v1_genomic.fna.gz | prodigal -d GCF_004402515.1_ASM440251v1_genomic.fna/cds.fna -a GCF_004402515.1_ASM440251v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:51,318] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:51,318] [INFO] Task started: HMMsearch
[2024-01-24 13:12:51,318] [INFO] Running command: hmmsearch --tblout GCF_004402515.1_ASM440251v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f203c63-7289-4565-ae5d-03aa7eefd499/dqc_reference/reference_markers.hmm GCF_004402515.1_ASM440251v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:51,629] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:51,634] [INFO] Found 6/6 markers.
[2024-01-24 13:12:51,666] [INFO] Query marker FASTA was written to GCF_004402515.1_ASM440251v1_genomic.fna/markers.fasta
[2024-01-24 13:12:51,666] [INFO] Task started: Blastn
[2024-01-24 13:12:51,667] [INFO] Running command: blastn -query GCF_004402515.1_ASM440251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f203c63-7289-4565-ae5d-03aa7eefd499/dqc_reference/reference_markers.fasta -out GCF_004402515.1_ASM440251v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:52,695] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:52,698] [INFO] Selected 13 target genomes.
[2024-01-24 13:12:52,698] [INFO] Target genome list was writen to GCF_004402515.1_ASM440251v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:52,704] [INFO] Task started: fastANI
[2024-01-24 13:12:52,704] [INFO] Running command: fastANI --query /var/lib/cwl/stgea599bdd-f521-4bfc-be49-de9ddbf051b8/GCF_004402515.1_ASM440251v1_genomic.fna.gz --refList GCF_004402515.1_ASM440251v1_genomic.fna/target_genomes.txt --output GCF_004402515.1_ASM440251v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:03,646] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:03,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f203c63-7289-4565-ae5d-03aa7eefd499/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:03,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f203c63-7289-4565-ae5d-03aa7eefd499/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:03,663] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:03,663] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:03,664] [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 luteum	strain=Hh15	GCA_004402515.1	1424661	1424661	type	True	100.0	1244	1247	95	conclusive
Cryobacterium luteum	strain=CGMCC 1.11210	GCA_900110125.1	1424661	1424661	type	True	99.9868	1226	1247	95	conclusive
Cryobacterium ruanii	strain=Sr36	GCA_004404055.1	1259197	1259197	type	True	87.2597	836	1247	95	below_threshold
Cryobacterium flavum	strain=Hh8	GCA_004402625.1	1424659	1424659	type	True	87.1338	907	1247	95	below_threshold
Cryobacterium flavum	strain=CGMCC 1.11215	GCA_900103805.1	1424659	1424659	type	True	87.1337	913	1247	95	below_threshold
Cryobacterium aureum	strain=Hh31	GCA_002954245.1	995037	995037	type	True	86.2268	911	1247	95	below_threshold
Cryobacterium levicorallinum	strain=Hh34	GCA_004402405.1	995038	995038	type	True	85.4782	788	1247	95	below_threshold
Cryobacterium levicorallinum	strain=NBRC 107883	GCA_007992355.1	995038	995038	type	True	85.4309	800	1247	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	85.3939	812	1247	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	80.4712	520	1247	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	77.8425	314	1247	95	below_threshold
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	77.4452	233	1247	95	below_threshold
Rathayibacter tanaceti	strain=VKM Ac-2596	GCA_001634385.1	1671680	1671680	type	True	77.2778	257	1247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:03,669] [INFO] DFAST Taxonomy check result was written to GCF_004402515.1_ASM440251v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:03,670] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:03,670] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:03,671] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f203c63-7289-4565-ae5d-03aa7eefd499/dqc_reference/checkm_data
[2024-01-24 13:13:03,672] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:03,710] [INFO] Task started: CheckM
[2024-01-24 13:13:03,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004402515.1_ASM440251v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004402515.1_ASM440251v1_genomic.fna/checkm_input GCF_004402515.1_ASM440251v1_genomic.fna/checkm_result
[2024-01-24 13:13:40,521] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:40,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:40,545] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:40,546] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:40,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004402515.1_ASM440251v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:40,547] [INFO] Task started: Blastn
[2024-01-24 13:13:40,547] [INFO] Running command: blastn -query GCF_004402515.1_ASM440251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f203c63-7289-4565-ae5d-03aa7eefd499/dqc_reference/reference_markers_gtdb.fasta -out GCF_004402515.1_ASM440251v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:42,123] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:42,126] [INFO] Selected 11 target genomes.
[2024-01-24 13:13:42,126] [INFO] Target genome list was writen to GCF_004402515.1_ASM440251v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:42,134] [INFO] Task started: fastANI
[2024-01-24 13:13:42,135] [INFO] Running command: fastANI --query /var/lib/cwl/stgea599bdd-f521-4bfc-be49-de9ddbf051b8/GCF_004402515.1_ASM440251v1_genomic.fna.gz --refList GCF_004402515.1_ASM440251v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004402515.1_ASM440251v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:51,966] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:51,983] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:51,983] [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_900110125.1	s__Cryobacterium luteum	99.9868	1226	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.76	99.53	0.96	0.95	3	conclusive
GCF_004402535.1	s__Cryobacterium sp004402535	89.9012	905	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004404055.1	s__Cryobacterium ruanii	87.2475	837	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103805.1	s__Cryobacterium flavum	87.1198	914	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.64	97.38	0.89	0.83	6	-
GCF_002954245.1	s__Cryobacterium aureum	86.2395	910	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751745.1	s__Cryobacterium sp015751745	85.8534	781	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403185.1	s__Cryobacterium sp004403185	85.6072	823	1247	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	85.4529	798	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.96	97.96	0.88	0.88	2	-
GCF_004402405.1	s__Cryobacterium levicorallinum	85.4515	791	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.20	96.46	0.88	0.78	9	-
GCF_002929495.1	s__Cryobacterium sp002929495	85.3321	824	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.09	97.09	0.88	0.88	2	-
GCF_002929825.1	s__Cryobacterium sp002929825	84.9962	810	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	95.15	95.07	0.83	0.81	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:51,985] [INFO] GTDB search result was written to GCF_004402515.1_ASM440251v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:51,986] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:51,992] [INFO] DFAST_QC result json was written to GCF_004402515.1_ASM440251v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:51,992] [INFO] DFAST_QC completed!
[2024-01-24 13:13:51,992] [INFO] Total running time: 0h1m14s