[2024-01-24 11:13:49,563] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:49,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:49,565] [INFO] DQC Reference Directory: /var/lib/cwl/stgc841753b-9b56-495e-9f5a-2d7081ea9bf2/dqc_reference
[2024-01-24 11:13:50,754] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:50,755] [INFO] Task started: Prodigal
[2024-01-24 11:13:50,756] [INFO] Running command: gunzip -c /var/lib/cwl/stga515a20f-a58e-4f3b-9a84-d7ebcd36d829/GCF_016863095.1_ASM1686309v1_genomic.fna.gz | prodigal -d GCF_016863095.1_ASM1686309v1_genomic.fna/cds.fna -a GCF_016863095.1_ASM1686309v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:14:15,984] [INFO] Task succeeded: Prodigal
[2024-01-24 11:14:15,985] [INFO] Task started: HMMsearch
[2024-01-24 11:14:15,985] [INFO] Running command: hmmsearch --tblout GCF_016863095.1_ASM1686309v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc841753b-9b56-495e-9f5a-2d7081ea9bf2/dqc_reference/reference_markers.hmm GCF_016863095.1_ASM1686309v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:14:16,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:14:16,372] [INFO] Found 6/6 markers.
[2024-01-24 11:14:16,445] [INFO] Query marker FASTA was written to GCF_016863095.1_ASM1686309v1_genomic.fna/markers.fasta
[2024-01-24 11:14:16,445] [INFO] Task started: Blastn
[2024-01-24 11:14:16,446] [INFO] Running command: blastn -query GCF_016863095.1_ASM1686309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc841753b-9b56-495e-9f5a-2d7081ea9bf2/dqc_reference/reference_markers.fasta -out GCF_016863095.1_ASM1686309v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:17,803] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:17,807] [INFO] Selected 20 target genomes.
[2024-01-24 11:14:17,808] [INFO] Target genome list was writen to GCF_016863095.1_ASM1686309v1_genomic.fna/target_genomes.txt
[2024-01-24 11:14:17,816] [INFO] Task started: fastANI
[2024-01-24 11:14:17,816] [INFO] Running command: fastANI --query /var/lib/cwl/stga515a20f-a58e-4f3b-9a84-d7ebcd36d829/GCF_016863095.1_ASM1686309v1_genomic.fna.gz --refList GCF_016863095.1_ASM1686309v1_genomic.fna/target_genomes.txt --output GCF_016863095.1_ASM1686309v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:57,302] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:57,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc841753b-9b56-495e-9f5a-2d7081ea9bf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:57,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc841753b-9b56-495e-9f5a-2d7081ea9bf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:57,322] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:14:57,323] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:14:57,323] [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
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	100.0	3067	3068	95	inconclusive
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	95.8511	2654	3068	95	inconclusive
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	94.2777	2448	3068	95	below_threshold
Microbispora rosea	strain=ATCC 12950	GCA_900156315.1	58117	58117	type	True	92.9148	2277	3068	95	below_threshold
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	92.8376	2265	3068	95	below_threshold
Microbispora bryophytorum	strain=NEAU-TX2-2	GCA_014712735.1	1460882	1460882	type	True	92.6546	2086	3068	95	below_threshold
Microbispora bryophytorum	strain=DSM 46710	GCA_006874465.1	1460882	1460882	type	True	92.6183	2089	3068	95	below_threshold
Microbispora camponoti	strain=2C-HV3	GCA_014712745.1	1677852	1677852	type	True	92.5868	2095	3068	95	below_threshold
Microbispora bryophytorum	strain=CGMCC 4.7138	GCA_014645855.1	1460882	1460882	type	True	92.5786	2108	3068	95	below_threshold
Microbispora hainanensis	strain=DSM 45428	GCA_006874475.1	568844	568844	type	True	92.2187	2238	3068	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	83.1124	1534	3068	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	82.6609	1199	3068	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.0975	1482	3068	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.8002	927	3068	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	79.3964	1417	3068	95	below_threshold
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	76.5854	850	3068	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	76.5214	814	3068	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	76.5078	852	3068	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	75.9609	398	3068	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	75.8951	568	3068	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:57,324] [INFO] DFAST Taxonomy check result was written to GCF_016863095.1_ASM1686309v1_genomic.fna/tc_result.tsv
[2024-01-24 11:14:57,325] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:57,325] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:57,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc841753b-9b56-495e-9f5a-2d7081ea9bf2/dqc_reference/checkm_data
[2024-01-24 11:14:57,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:57,411] [INFO] Task started: CheckM
[2024-01-24 11:14:57,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863095.1_ASM1686309v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863095.1_ASM1686309v1_genomic.fna/checkm_input GCF_016863095.1_ASM1686309v1_genomic.fna/checkm_result
[2024-01-24 11:16:26,999] [INFO] Task succeeded: CheckM
[2024-01-24 11:16:27,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:16:27,021] [INFO] ===== Completeness check finished =====
[2024-01-24 11:16:27,021] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:16:27,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863095.1_ASM1686309v1_genomic.fna/markers.fasta)
[2024-01-24 11:16:27,022] [INFO] Task started: Blastn
[2024-01-24 11:16:27,022] [INFO] Running command: blastn -query GCF_016863095.1_ASM1686309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc841753b-9b56-495e-9f5a-2d7081ea9bf2/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863095.1_ASM1686309v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:16:29,112] [INFO] Task succeeded: Blastn
[2024-01-24 11:16:29,117] [INFO] Selected 13 target genomes.
[2024-01-24 11:16:29,117] [INFO] Target genome list was writen to GCF_016863095.1_ASM1686309v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:16:29,157] [INFO] Task started: fastANI
[2024-01-24 11:16:29,157] [INFO] Running command: fastANI --query /var/lib/cwl/stga515a20f-a58e-4f3b-9a84-d7ebcd36d829/GCF_016863095.1_ASM1686309v1_genomic.fna.gz --refList GCF_016863095.1_ASM1686309v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863095.1_ASM1686309v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:16:55,034] [INFO] Task succeeded: fastANI
[2024-01-24 11:16:55,049] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:16:55,049] [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_016863095.1	s__Microbispora siamensis	100.0	3067	3068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.99	95.83	0.88	0.87	3	conclusive
GCF_006334915.2	s__Microbispora catharanthi	94.2497	2453	3068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.79	95.45	0.89	0.84	4	-
GCF_900156315.1	s__Microbispora rosea	92.8951	2278	3068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.16	98.33	0.97	0.94	3	-
GCF_006874465.1	s__Microbispora bryophytorum	92.6042	2090	3068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.22	97.66	0.97	0.91	4	-
GCF_006874475.1	s__Microbispora hainanensis	92.2127	2239	3068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	95.41	95.40	0.85	0.85	4	-
GCF_014161445.1	s__Microbispora sp014161445	91.6855	2248	3068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.71	98.71	0.93	0.93	2	-
GCF_014647835.1	s__Microbispora aerata	90.4708	1835	3068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012999535.1	s__Microbispora sp012999535	90.012	1984	3068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003260025.2	s__Microbispora triticiradicis	88.0708	1862	3068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.16	96.98	0.92	0.88	7	-
GCF_014596515.1	s__Kitasatospora sp014596515	76.4886	790	3068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826085.1	s__Nigerium massiliense	76.158	293	3068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Nigerium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004912155.1	s__Glycomyces paridis	75.8819	574	3068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242625.1	s__JAFEBO01 sp018242625	74.7849	70	3068	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAFEBO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:16:55,051] [INFO] GTDB search result was written to GCF_016863095.1_ASM1686309v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:16:55,052] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:16:55,055] [INFO] DFAST_QC result json was written to GCF_016863095.1_ASM1686309v1_genomic.fna/dqc_result.json
[2024-01-24 11:16:55,056] [INFO] DFAST_QC completed!
[2024-01-24 11:16:55,056] [INFO] Total running time: 0h3m5s