[2024-01-24 14:10:16,183] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:10:16,185] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:10:16,186] [INFO] DQC Reference Directory: /var/lib/cwl/stgb935a4d4-32b9-4a9f-a4af-7b6267b5cdee/dqc_reference
[2024-01-24 14:10:17,459] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:10:17,460] [INFO] Task started: Prodigal
[2024-01-24 14:10:17,460] [INFO] Running command: gunzip -c /var/lib/cwl/stg6808e7ef-211e-4455-af8b-4302e4360df5/GCF_022760445.1_ASM2276044v1_genomic.fna.gz | prodigal -d GCF_022760445.1_ASM2276044v1_genomic.fna/cds.fna -a GCF_022760445.1_ASM2276044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:10:30,123] [INFO] Task succeeded: Prodigal
[2024-01-24 14:10:30,123] [INFO] Task started: HMMsearch
[2024-01-24 14:10:30,123] [INFO] Running command: hmmsearch --tblout GCF_022760445.1_ASM2276044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb935a4d4-32b9-4a9f-a4af-7b6267b5cdee/dqc_reference/reference_markers.hmm GCF_022760445.1_ASM2276044v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:10:30,422] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:10:30,424] [INFO] Found 6/6 markers.
[2024-01-24 14:10:30,467] [INFO] Query marker FASTA was written to GCF_022760445.1_ASM2276044v1_genomic.fna/markers.fasta
[2024-01-24 14:10:30,467] [INFO] Task started: Blastn
[2024-01-24 14:10:30,467] [INFO] Running command: blastn -query GCF_022760445.1_ASM2276044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb935a4d4-32b9-4a9f-a4af-7b6267b5cdee/dqc_reference/reference_markers.fasta -out GCF_022760445.1_ASM2276044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:31,700] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:31,703] [INFO] Selected 17 target genomes.
[2024-01-24 14:10:31,704] [INFO] Target genome list was writen to GCF_022760445.1_ASM2276044v1_genomic.fna/target_genomes.txt
[2024-01-24 14:10:31,709] [INFO] Task started: fastANI
[2024-01-24 14:10:31,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg6808e7ef-211e-4455-af8b-4302e4360df5/GCF_022760445.1_ASM2276044v1_genomic.fna.gz --refList GCF_022760445.1_ASM2276044v1_genomic.fna/target_genomes.txt --output GCF_022760445.1_ASM2276044v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:10:44,674] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:44,675] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb935a4d4-32b9-4a9f-a4af-7b6267b5cdee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:10:44,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb935a4d4-32b9-4a9f-a4af-7b6267b5cdee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:10:44,690] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:10:44,691] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:10:44,691] [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 zongtaii	strain=TMN-42	GCA_002909375.1	1259217	1259217	type	True	81.2275	618	1462	95	below_threshold
Cryobacterium breve	strain=TMT4-23	GCA_004402375.1	1259258	1259258	type	True	81.1397	605	1462	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	81.0959	576	1462	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	81.0908	679	1462	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_004564325.1	386301	386301	type	True	81.0476	570	1462	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	80.988	670	1462	95	below_threshold
Cryobacterium melibiosiphilum	strain=Hh39	GCA_003602235.1	995039	995039	type	True	80.474	590	1462	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	80.279	458	1462	95	below_threshold
Cryobacterium luteum	strain=Hh15	GCA_004402515.1	1424661	1424661	type	True	79.7847	527	1462	95	below_threshold
Cryobacterium luteum	strain=CGMCC 1.11210	GCA_900110125.1	1424661	1424661	type	True	79.7637	532	1462	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	79.7266	522	1462	95	below_threshold
Cryobacterium flavum	strain=CGMCC 1.11215	GCA_900103805.1	1424659	1424659	type	True	79.6745	547	1462	95	below_threshold
Cryobacterium ruanii	strain=Sr36	GCA_004404055.1	1259197	1259197	type	True	79.5679	488	1462	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.7398	464	1462	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.5435	397	1462	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.4885	435	1462	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.3957	448	1462	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:10:44,693] [INFO] DFAST Taxonomy check result was written to GCF_022760445.1_ASM2276044v1_genomic.fna/tc_result.tsv
[2024-01-24 14:10:44,693] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:10:44,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:10:44,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb935a4d4-32b9-4a9f-a4af-7b6267b5cdee/dqc_reference/checkm_data
[2024-01-24 14:10:44,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:10:44,741] [INFO] Task started: CheckM
[2024-01-24 14:10:44,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022760445.1_ASM2276044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022760445.1_ASM2276044v1_genomic.fna/checkm_input GCF_022760445.1_ASM2276044v1_genomic.fna/checkm_result
[2024-01-24 14:11:24,456] [INFO] Task succeeded: CheckM
[2024-01-24 14:11:24,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:11:24,471] [INFO] ===== Completeness check finished =====
[2024-01-24 14:11:24,472] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:11:24,472] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022760445.1_ASM2276044v1_genomic.fna/markers.fasta)
[2024-01-24 14:11:24,472] [INFO] Task started: Blastn
[2024-01-24 14:11:24,473] [INFO] Running command: blastn -query GCF_022760445.1_ASM2276044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb935a4d4-32b9-4a9f-a4af-7b6267b5cdee/dqc_reference/reference_markers_gtdb.fasta -out GCF_022760445.1_ASM2276044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:11:26,360] [INFO] Task succeeded: Blastn
[2024-01-24 14:11:26,363] [INFO] Selected 10 target genomes.
[2024-01-24 14:11:26,363] [INFO] Target genome list was writen to GCF_022760445.1_ASM2276044v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:11:26,382] [INFO] Task started: fastANI
[2024-01-24 14:11:26,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg6808e7ef-211e-4455-af8b-4302e4360df5/GCF_022760445.1_ASM2276044v1_genomic.fna.gz --refList GCF_022760445.1_ASM2276044v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022760445.1_ASM2276044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:11:35,372] [INFO] Task succeeded: fastANI
[2024-01-24 14:11:35,384] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:11:35,384] [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_004402485.1	s__Cryobacterium sp004402485	97.907	1219	1462	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_004402235.1	s__Cryobacterium sp004402235	91.7379	1080	1462	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.29	99.21	0.93	0.91	7	-
GCF_004403515.1	s__Cryobacterium sp004403515	82.5124	654	1462	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402495.1	s__Cryobacterium sp004402495	82.4943	740	1462	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.47	98.47	0.92	0.92	2	-
GCF_015752155.1	s__Cryobacterium sp015752155	82.4149	783	1462	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402595.1	s__Cryobacterium sp004402595	81.8424	676	1462	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.65	99.58	0.91	0.90	6	-
GCF_004402785.1	s__Cryobacterium sp004402785	81.5837	702	1462	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403065.1	s__Cryobacterium sp004403065	81.5061	657	1462	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	81.3842	604	1462	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	80.9856	671	1462	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 14:11:35,386] [INFO] GTDB search result was written to GCF_022760445.1_ASM2276044v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:11:35,386] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:11:35,390] [INFO] DFAST_QC result json was written to GCF_022760445.1_ASM2276044v1_genomic.fna/dqc_result.json
[2024-01-24 14:11:35,390] [INFO] DFAST_QC completed!
[2024-01-24 14:11:35,390] [INFO] Total running time: 0h1m19s