[2024-01-24 13:58:41,639] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:41,641] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:41,641] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b0d054e-b827-4c7d-a72f-08bc712ca6fb/dqc_reference
[2024-01-24 13:58:42,957] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:42,958] [INFO] Task started: Prodigal
[2024-01-24 13:58:42,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg95225067-1612-4efe-afd6-cdd67c85d7f3/GCF_004403305.1_ASM440330v1_genomic.fna.gz | prodigal -d GCF_004403305.1_ASM440330v1_genomic.fna/cds.fna -a GCF_004403305.1_ASM440330v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:55,885] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:55,886] [INFO] Task started: HMMsearch
[2024-01-24 13:58:55,886] [INFO] Running command: hmmsearch --tblout GCF_004403305.1_ASM440330v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b0d054e-b827-4c7d-a72f-08bc712ca6fb/dqc_reference/reference_markers.hmm GCF_004403305.1_ASM440330v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:56,318] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:56,319] [INFO] Found 6/6 markers.
[2024-01-24 13:58:56,364] [INFO] Query marker FASTA was written to GCF_004403305.1_ASM440330v1_genomic.fna/markers.fasta
[2024-01-24 13:58:56,364] [INFO] Task started: Blastn
[2024-01-24 13:58:56,364] [INFO] Running command: blastn -query GCF_004403305.1_ASM440330v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b0d054e-b827-4c7d-a72f-08bc712ca6fb/dqc_reference/reference_markers.fasta -out GCF_004403305.1_ASM440330v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:57,429] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:57,432] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:57,433] [INFO] Target genome list was writen to GCF_004403305.1_ASM440330v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:57,452] [INFO] Task started: fastANI
[2024-01-24 13:58:57,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg95225067-1612-4efe-afd6-cdd67c85d7f3/GCF_004403305.1_ASM440330v1_genomic.fna.gz --refList GCF_004403305.1_ASM440330v1_genomic.fna/target_genomes.txt --output GCF_004403305.1_ASM440330v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:13,677] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:13,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b0d054e-b827-4c7d-a72f-08bc712ca6fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:13,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b0d054e-b827-4c7d-a72f-08bc712ca6fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:13,694] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:59:13,694] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:59:13,694] [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 melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	87.4212	1055	1411	95	below_threshold
Cryobacterium flavum	strain=CGMCC 1.11215	GCA_900103805.1	1424659	1424659	type	True	81.7284	684	1411	95	below_threshold
Cryobacterium luteum	strain=Hh15	GCA_004402515.1	1424661	1424661	type	True	81.6474	665	1411	95	below_threshold
Cryobacterium luteum	strain=CGMCC 1.11210	GCA_900110125.1	1424661	1424661	type	True	81.5518	673	1411	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	81.409	615	1411	95	below_threshold
Cryobacterium levicorallinum	strain=Hh34	GCA_004402405.1	995038	995038	type	True	81.3766	625	1411	95	below_threshold
Cryobacterium levicorallinum	strain=NBRC 107883	GCA_007992355.1	995038	995038	type	True	81.3589	613	1411	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	80.5434	553	1411	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	80.4798	551	1411	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	80.4217	549	1411	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	80.3917	594	1411	95	below_threshold
Cryobacterium roopkundense	strain=RuG17	GCA_000764165.1	1001240	1001240	type	True	80.3695	635	1411	95	below_threshold
Cryobacterium roopkundense	strain=DSM 21065	GCA_014200405.1	1001240	1001240	type	True	80.3288	678	1411	95	below_threshold
Cryobacterium zongtaii	strain=TMN-42	GCA_002909375.1	1259217	1259217	type	True	80.2824	562	1411	95	below_threshold
Cryobacterium psychrophilum	strain=DSM 4854	GCA_004365915.1	41988	41988	type	True	80.1545	533	1411	95	below_threshold
Cryobacterium breve	strain=TMT4-23	GCA_004402375.1	1259258	1259258	type	True	79.9425	551	1411	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.3265	385	1411	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.3045	409	1411	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.2364	387	1411	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.2085	393	1411	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:13,696] [INFO] DFAST Taxonomy check result was written to GCF_004403305.1_ASM440330v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:13,697] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:13,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:13,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b0d054e-b827-4c7d-a72f-08bc712ca6fb/dqc_reference/checkm_data
[2024-01-24 13:59:13,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:13,746] [INFO] Task started: CheckM
[2024-01-24 13:59:13,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004403305.1_ASM440330v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004403305.1_ASM440330v1_genomic.fna/checkm_input GCF_004403305.1_ASM440330v1_genomic.fna/checkm_result
[2024-01-24 13:59:54,552] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:54,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:54,573] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:54,573] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:54,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004403305.1_ASM440330v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:54,574] [INFO] Task started: Blastn
[2024-01-24 13:59:54,574] [INFO] Running command: blastn -query GCF_004403305.1_ASM440330v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b0d054e-b827-4c7d-a72f-08bc712ca6fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_004403305.1_ASM440330v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:56,278] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:56,283] [INFO] Selected 19 target genomes.
[2024-01-24 13:59:56,283] [INFO] Target genome list was writen to GCF_004403305.1_ASM440330v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:56,316] [INFO] Task started: fastANI
[2024-01-24 13:59:56,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg95225067-1612-4efe-afd6-cdd67c85d7f3/GCF_004403305.1_ASM440330v1_genomic.fna.gz --refList GCF_004403305.1_ASM440330v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004403305.1_ASM440330v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:11,995] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:12,013] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:12,013] [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_004403305.1	s__Cryobacterium sp004403305	100.0	1406	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003602235.1	s__Cryobacterium sp003602235	87.4265	1055	1411	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	81.5493	674	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.76	99.53	0.96	0.95	3	-
GCF_004402405.1	s__Cryobacterium levicorallinum	81.3437	628	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.20	96.46	0.88	0.78	9	-
GCF_004403985.1	s__Cryobacterium sp004403985	80.9846	582	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.96	97.96	0.88	0.88	2	-
GCF_004402215.1	s__Cryobacterium sp004402215	80.6879	577	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403395.1	s__Cryobacterium sp004403395	80.5988	540	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003185895.1	s__Cryobacterium arcticum	80.5767	550	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752155.1	s__Cryobacterium sp015752155	80.5677	621	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929555.1	s__Cryobacterium sp002929555	80.5043	589	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101115.1	s__Cryobacterium psychrotolerans	80.4397	546	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.25	98.21	0.94	0.88	4	-
GCF_014200405.1	s__Cryobacterium roopkundense	80.3549	675	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004210215.1	s__Cryobacterium sp004210215	80.3484	536	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403945.1	s__Cryobacterium sp004403945	80.3374	587	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402695.1	s__Cryobacterium sp004402695	80.3215	564	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403465.1	s__Cryobacterium sp004403465	80.2298	570	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.40	99.40	0.93	0.93	2	-
GCF_004365915.1	s__Cryobacterium psychrophilum	80.1239	536	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002929845.1	s__Cryobacterium sp002929845	79.9822	553	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.90	95.88	0.91	0.88	15	-
GCF_000738085.1	s__Cryobacterium sp000738085	79.9366	517	1411	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 14:00:12,019] [INFO] GTDB search result was written to GCF_004403305.1_ASM440330v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:12,020] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:12,030] [INFO] DFAST_QC result json was written to GCF_004403305.1_ASM440330v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:12,030] [INFO] DFAST_QC completed!
[2024-01-24 14:00:12,030] [INFO] Total running time: 0h1m30s