[2024-01-24 14:40:02,571] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:40:02,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:40:02,573] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0892a64-20f0-4e0e-8da3-0a6eafeffb89/dqc_reference
[2024-01-24 14:40:03,960] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:40:03,964] [INFO] Task started: Prodigal
[2024-01-24 14:40:03,964] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f707b74-44c2-47b4-8acb-9e3a75ee5a2e/GCF_014200405.1_ASM1420040v1_genomic.fna.gz | prodigal -d GCF_014200405.1_ASM1420040v1_genomic.fna/cds.fna -a GCF_014200405.1_ASM1420040v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:18,994] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:18,994] [INFO] Task started: HMMsearch
[2024-01-24 14:40:18,994] [INFO] Running command: hmmsearch --tblout GCF_014200405.1_ASM1420040v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0892a64-20f0-4e0e-8da3-0a6eafeffb89/dqc_reference/reference_markers.hmm GCF_014200405.1_ASM1420040v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:19,285] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:19,287] [INFO] Found 6/6 markers.
[2024-01-24 14:40:19,332] [INFO] Query marker FASTA was written to GCF_014200405.1_ASM1420040v1_genomic.fna/markers.fasta
[2024-01-24 14:40:19,332] [INFO] Task started: Blastn
[2024-01-24 14:40:19,332] [INFO] Running command: blastn -query GCF_014200405.1_ASM1420040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0892a64-20f0-4e0e-8da3-0a6eafeffb89/dqc_reference/reference_markers.fasta -out GCF_014200405.1_ASM1420040v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:20,376] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:20,381] [INFO] Selected 17 target genomes.
[2024-01-24 14:40:20,381] [INFO] Target genome list was writen to GCF_014200405.1_ASM1420040v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:20,389] [INFO] Task started: fastANI
[2024-01-24 14:40:20,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f707b74-44c2-47b4-8acb-9e3a75ee5a2e/GCF_014200405.1_ASM1420040v1_genomic.fna.gz --refList GCF_014200405.1_ASM1420040v1_genomic.fna/target_genomes.txt --output GCF_014200405.1_ASM1420040v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:35,127] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:35,127] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0892a64-20f0-4e0e-8da3-0a6eafeffb89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:35,127] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0892a64-20f0-4e0e-8da3-0a6eafeffb89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:35,142] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:40:35,142] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:35,142] [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 roopkundense	strain=DSM 21065	GCA_014200405.1	1001240	1001240	type	True	100.0	1507	1510	95	conclusive
Cryobacterium roopkundense	strain=RuG17	GCA_000764165.1	1001240	1001240	type	True	99.883	1318	1510	95	conclusive
Cryobacterium psychrophilum	strain=DSM 4854	GCA_004365915.1	41988	41988	type	True	81.5517	674	1510	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	80.9056	595	1510	95	below_threshold
Cryobacterium melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	80.573	656	1510	95	below_threshold
Cryobacterium flavum	strain=Hh8	GCA_004402625.1	1424659	1424659	type	True	80.5489	645	1510	95	below_threshold
Cryobacterium flavum	strain=CGMCC 1.11215	GCA_900103805.1	1424659	1424659	type	True	80.539	633	1510	95	below_threshold
Cryobacterium luteum	strain=Hh15	GCA_004402515.1	1424661	1424661	type	True	80.423	609	1510	95	below_threshold
Cryobacterium luteum	strain=CGMCC 1.11210	GCA_900110125.1	1424661	1424661	type	True	80.3809	614	1510	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	79.9823	524	1510	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	79.8445	512	1510	95	below_threshold
Cryobacterium zongtaii	strain=TMN-42	GCA_002909375.1	1259217	1259217	type	True	79.7737	514	1510	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	79.7551	517	1510	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	79.6983	510	1510	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	77.9552	304	1510	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	77.9399	309	1510	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.7626	360	1510	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:35,144] [INFO] DFAST Taxonomy check result was written to GCF_014200405.1_ASM1420040v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:35,145] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:35,145] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:35,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0892a64-20f0-4e0e-8da3-0a6eafeffb89/dqc_reference/checkm_data
[2024-01-24 14:40:35,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:35,196] [INFO] Task started: CheckM
[2024-01-24 14:40:35,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014200405.1_ASM1420040v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014200405.1_ASM1420040v1_genomic.fna/checkm_input GCF_014200405.1_ASM1420040v1_genomic.fna/checkm_result
[2024-01-24 14:41:19,041] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:19,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:19,066] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:19,066] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:19,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014200405.1_ASM1420040v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:19,067] [INFO] Task started: Blastn
[2024-01-24 14:41:19,067] [INFO] Running command: blastn -query GCF_014200405.1_ASM1420040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0892a64-20f0-4e0e-8da3-0a6eafeffb89/dqc_reference/reference_markers_gtdb.fasta -out GCF_014200405.1_ASM1420040v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:20,525] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:20,530] [INFO] Selected 12 target genomes.
[2024-01-24 14:41:20,530] [INFO] Target genome list was writen to GCF_014200405.1_ASM1420040v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:20,539] [INFO] Task started: fastANI
[2024-01-24 14:41:20,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f707b74-44c2-47b4-8acb-9e3a75ee5a2e/GCF_014200405.1_ASM1420040v1_genomic.fna.gz --refList GCF_014200405.1_ASM1420040v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014200405.1_ASM1420040v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:31,725] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:31,735] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:31,735] [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_014200405.1	s__Cryobacterium roopkundense	100.0	1509	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000738085.1	s__Cryobacterium sp000738085	83.6571	845	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365915.1	s__Cryobacterium psychrophilum	81.5718	673	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003602235.1	s__Cryobacterium sp003602235	80.5668	657	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403305.1	s__Cryobacterium sp004403305	80.5402	644	1510	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	80.1869	542	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679725.1	s__Cryobacterium arcticum_A	80.1477	533	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402215.1	s__Cryobacterium sp004402215	80.0996	530	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929495.1	s__Cryobacterium sp002929495	79.9357	533	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.09	97.09	0.88	0.88	2	-
GCF_004402595.1	s__Cryobacterium sp004402595	79.8721	515	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.65	99.58	0.91	0.90	6	-
GCF_900101115.1	s__Cryobacterium psychrotolerans	79.8389	511	1510	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.25	98.21	0.94	0.88	4	-
GCF_002929555.1	s__Cryobacterium sp002929555	79.8041	525	1510	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 14:41:31,745] [INFO] GTDB search result was written to GCF_014200405.1_ASM1420040v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:31,745] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:31,749] [INFO] DFAST_QC result json was written to GCF_014200405.1_ASM1420040v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:31,749] [INFO] DFAST_QC completed!
[2024-01-24 14:41:31,750] [INFO] Total running time: 0h1m29s