[2024-01-24 11:35:11,353] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,355] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg22c9f96a-3d22-43da-8390-fb3d31187ded/dqc_reference
[2024-01-24 11:35:12,750] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:12,750] [INFO] Task started: Prodigal
[2024-01-24 11:35:12,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg3816fdf0-ac8b-49ee-ad21-3d201a19f2e0/GCF_008728085.1_ASM872808v1_genomic.fna.gz | prodigal -d GCF_008728085.1_ASM872808v1_genomic.fna/cds.fna -a GCF_008728085.1_ASM872808v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:37,012] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:37,013] [INFO] Task started: HMMsearch
[2024-01-24 11:35:37,013] [INFO] Running command: hmmsearch --tblout GCF_008728085.1_ASM872808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22c9f96a-3d22-43da-8390-fb3d31187ded/dqc_reference/reference_markers.hmm GCF_008728085.1_ASM872808v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:37,443] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:37,444] [INFO] Found 6/6 markers.
[2024-01-24 11:35:37,508] [INFO] Query marker FASTA was written to GCF_008728085.1_ASM872808v1_genomic.fna/markers.fasta
[2024-01-24 11:35:37,508] [INFO] Task started: Blastn
[2024-01-24 11:35:37,509] [INFO] Running command: blastn -query GCF_008728085.1_ASM872808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22c9f96a-3d22-43da-8390-fb3d31187ded/dqc_reference/reference_markers.fasta -out GCF_008728085.1_ASM872808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:38,911] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:38,914] [INFO] Selected 16 target genomes.
[2024-01-24 11:35:38,914] [INFO] Target genome list was writen to GCF_008728085.1_ASM872808v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:38,922] [INFO] Task started: fastANI
[2024-01-24 11:35:38,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg3816fdf0-ac8b-49ee-ad21-3d201a19f2e0/GCF_008728085.1_ASM872808v1_genomic.fna.gz --refList GCF_008728085.1_ASM872808v1_genomic.fna/target_genomes.txt --output GCF_008728085.1_ASM872808v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:13,880] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:13,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22c9f96a-3d22-43da-8390-fb3d31187ded/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:13,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22c9f96a-3d22-43da-8390-fb3d31187ded/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:13,898] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:36:13,898] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:36:13,899] [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 cellulosiformans	strain=Gxj-6	GCA_008728085.1	2614688	2614688	type	True	100.0	2778	2785	95	inconclusive
Microbispora amethystogenes	strain=NBRC 101907	GCA_016863015.1	1427754	1427754	type	True	97.4015	2391	2785	95	inconclusive
Microbispora fusca	strain=NEAU-HEGS1-5	GCA_005864065.1	2576905	2576905	type	True	94.5089	2252	2785	95	below_threshold
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	87.9175	1975	2785	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	87.7706	1912	2785	95	below_threshold
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	87.6062	1941	2785	95	below_threshold
Microbispora bryophytorum	strain=DSM 46710	GCA_006874465.1	1460882	1460882	type	True	87.4513	1840	2785	95	below_threshold
Microbispora camponoti	strain=2C-HV3	GCA_014712745.1	1677852	1677852	type	True	87.3639	1845	2785	95	below_threshold
Microbispora hainanensis	strain=DSM 45428	GCA_006874475.1	568844	568844	type	True	87.1342	1889	2785	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	86.957	1608	2785	95	below_threshold
Microbispora rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	86.9172	1628	2785	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	83.129	1482	2785	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	82.1691	1131	2785	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.7201	1303	2785	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.5969	839	2785	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.3007	1264	2785	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:13,900] [INFO] DFAST Taxonomy check result was written to GCF_008728085.1_ASM872808v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:13,901] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:13,901] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:13,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22c9f96a-3d22-43da-8390-fb3d31187ded/dqc_reference/checkm_data
[2024-01-24 11:36:13,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:13,982] [INFO] Task started: CheckM
[2024-01-24 11:36:13,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008728085.1_ASM872808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008728085.1_ASM872808v1_genomic.fna/checkm_input GCF_008728085.1_ASM872808v1_genomic.fna/checkm_result
[2024-01-24 11:37:30,889] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:30,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:30,919] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:30,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:30,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008728085.1_ASM872808v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:30,920] [INFO] Task started: Blastn
[2024-01-24 11:37:30,920] [INFO] Running command: blastn -query GCF_008728085.1_ASM872808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22c9f96a-3d22-43da-8390-fb3d31187ded/dqc_reference/reference_markers_gtdb.fasta -out GCF_008728085.1_ASM872808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:33,023] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:33,027] [INFO] Selected 11 target genomes.
[2024-01-24 11:37:33,027] [INFO] Target genome list was writen to GCF_008728085.1_ASM872808v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:33,080] [INFO] Task started: fastANI
[2024-01-24 11:37:33,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg3816fdf0-ac8b-49ee-ad21-3d201a19f2e0/GCF_008728085.1_ASM872808v1_genomic.fna.gz --refList GCF_008728085.1_ASM872808v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008728085.1_ASM872808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:57,590] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:57,605] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:57,605] [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_016863015.1	s__Microbispora amethystogenes	97.411	2390	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.43	97.43	0.91	0.91	2	conclusive
GCA_003260025.2	s__Microbispora triticiradicis	94.3202	2138	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.16	96.98	0.92	0.88	7	-
GCF_006334915.2	s__Microbispora catharanthi	87.9026	1978	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.79	95.45	0.89	0.84	4	-
GCF_014161445.1	s__Microbispora sp014161445	87.8203	1923	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.71	98.71	0.93	0.93	2	-
GCF_016863095.1	s__Microbispora siamensis	87.7883	1909	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.99	95.83	0.88	0.87	3	-
GCF_006874465.1	s__Microbispora bryophytorum	87.4406	1841	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.22	97.66	0.97	0.91	4	-
GCF_900156315.1	s__Microbispora rosea	87.4023	1951	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.16	98.33	0.97	0.94	3	-
GCF_006874475.1	s__Microbispora hainanensis	87.1329	1888	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	95.41	95.40	0.85	0.85	4	-
GCF_012999535.1	s__Microbispora sp012999535	86.9461	1785	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647835.1	s__Microbispora aerata	86.921	1628	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001570365.1	s__Microtetraspora fusca	81.1355	1351	2785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:57,607] [INFO] GTDB search result was written to GCF_008728085.1_ASM872808v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:57,607] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:57,611] [INFO] DFAST_QC result json was written to GCF_008728085.1_ASM872808v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:57,611] [INFO] DFAST_QC completed!
[2024-01-24 11:37:57,611] [INFO] Total running time: 0h2m46s