[2024-01-25 18:09:05,854] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:05,856] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:05,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg79b1ed5a-874f-4780-8e0c-214938ae6e0c/dqc_reference
[2024-01-25 18:09:07,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:07,026] [INFO] Task started: Prodigal
[2024-01-25 18:09:07,027] [INFO] Running command: gunzip -c /var/lib/cwl/stg922741d9-9162-4848-affb-16f27adf3139/GCF_025960885.1_ASM2596088v1_genomic.fna.gz | prodigal -d GCF_025960885.1_ASM2596088v1_genomic.fna/cds.fna -a GCF_025960885.1_ASM2596088v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:16,367] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:16,367] [INFO] Task started: HMMsearch
[2024-01-25 18:09:16,367] [INFO] Running command: hmmsearch --tblout GCF_025960885.1_ASM2596088v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79b1ed5a-874f-4780-8e0c-214938ae6e0c/dqc_reference/reference_markers.hmm GCF_025960885.1_ASM2596088v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:16,562] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:16,563] [INFO] Found 6/6 markers.
[2024-01-25 18:09:16,593] [INFO] Query marker FASTA was written to GCF_025960885.1_ASM2596088v1_genomic.fna/markers.fasta
[2024-01-25 18:09:16,593] [INFO] Task started: Blastn
[2024-01-25 18:09:16,593] [INFO] Running command: blastn -query GCF_025960885.1_ASM2596088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79b1ed5a-874f-4780-8e0c-214938ae6e0c/dqc_reference/reference_markers.fasta -out GCF_025960885.1_ASM2596088v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:17,650] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:17,652] [INFO] Selected 14 target genomes.
[2024-01-25 18:09:17,653] [INFO] Target genome list was writen to GCF_025960885.1_ASM2596088v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:17,663] [INFO] Task started: fastANI
[2024-01-25 18:09:17,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg922741d9-9162-4848-affb-16f27adf3139/GCF_025960885.1_ASM2596088v1_genomic.fna.gz --refList GCF_025960885.1_ASM2596088v1_genomic.fna/target_genomes.txt --output GCF_025960885.1_ASM2596088v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:28,629] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:28,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79b1ed5a-874f-4780-8e0c-214938ae6e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:28,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79b1ed5a-874f-4780-8e0c-214938ae6e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:28,639] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:09:28,639] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:09:28,639] [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
Microbacterium enclense	strain=NIO-1002	GCA_900096885.1	993073	993073	type	True	86.3282	866	1257	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_001456955.1	993073	993073	type	True	86.3217	866	1257	95	below_threshold
Microbacterium testaceum	strain=NBRC 12675	GCA_006539145.1	2033	2033	suspected-type	True	86.0723	893	1257	95	below_threshold
Microbacterium proteolyticum	strain=CECT 8356	GCA_014192415.1	1572644	1572644	type	True	85.5892	878	1257	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	81.053	560	1257	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.9172	577	1257	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	80.8292	584	1257	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.7954	567	1257	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	80.6604	574	1257	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	80.6157	549	1257	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.5727	580	1257	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.3377	569	1257	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	80.113	506	1257	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	80.1043	510	1257	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:28,641] [INFO] DFAST Taxonomy check result was written to GCF_025960885.1_ASM2596088v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:28,642] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:28,642] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:28,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79b1ed5a-874f-4780-8e0c-214938ae6e0c/dqc_reference/checkm_data
[2024-01-25 18:09:28,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:28,681] [INFO] Task started: CheckM
[2024-01-25 18:09:28,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025960885.1_ASM2596088v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025960885.1_ASM2596088v1_genomic.fna/checkm_input GCF_025960885.1_ASM2596088v1_genomic.fna/checkm_result
[2024-01-25 18:10:21,376] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:21,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:21,395] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:21,395] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:21,396] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025960885.1_ASM2596088v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:21,396] [INFO] Task started: Blastn
[2024-01-25 18:10:21,396] [INFO] Running command: blastn -query GCF_025960885.1_ASM2596088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79b1ed5a-874f-4780-8e0c-214938ae6e0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_025960885.1_ASM2596088v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:23,158] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:23,163] [INFO] Selected 12 target genomes.
[2024-01-25 18:10:23,163] [INFO] Target genome list was writen to GCF_025960885.1_ASM2596088v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:23,178] [INFO] Task started: fastANI
[2024-01-25 18:10:23,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg922741d9-9162-4848-affb-16f27adf3139/GCF_025960885.1_ASM2596088v1_genomic.fna.gz --refList GCF_025960885.1_ASM2596088v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025960885.1_ASM2596088v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:33,636] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:33,646] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:33,646] [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_004854025.1	s__Microbacterium hydrothermale	97.1851	1041	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900156435.1	s__Microbacterium sp900156435	88.5301	950	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003075375.1	s__Microbacterium testaceum_E	87.2851	850	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.83	96.83	0.84	0.84	2	-
GCF_007679045.1	s__Microbacterium sp007679045	86.7392	917	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.00	99.00	0.94	0.94	2	-
GCF_008763945.1	s__Microbacterium testaceum_G	86.615	886	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104345.1	s__Microbacterium testaceum_A	86.5246	885	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.34	95.96	0.91	0.90	3	-
GCF_001456955.1	s__Microbacterium enclense	86.3009	868	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.78	97.57	0.95	0.89	3	-
GCF_006539145.1	s__Microbacterium testaceum	86.0697	893	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.70	98.67	0.94	0.93	3	-
GCF_017833635.1	s__Microbacterium sp017833635	85.858	872	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476285.1	s__Microbacterium testaceum_B	85.6994	838	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.43	98.38	0.88	0.88	4	-
GCF_014192415.1	s__Microbacterium proteolyticum	85.6019	877	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870695.1	s__Microbacterium sp016870695	83.9162	524	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:33,650] [INFO] GTDB search result was written to GCF_025960885.1_ASM2596088v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:33,651] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:33,654] [INFO] DFAST_QC result json was written to GCF_025960885.1_ASM2596088v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:33,655] [INFO] DFAST_QC completed!
[2024-01-25 18:10:33,655] [INFO] Total running time: 0h1m28s