[2024-01-24 15:03:15,303] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:15,304] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:15,304] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d1fea62-81fe-4859-9af1-ea302dc21376/dqc_reference
[2024-01-24 15:03:16,580] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:16,580] [INFO] Task started: Prodigal
[2024-01-24 15:03:16,581] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b224a73-4c20-4080-9fa7-e799c156e3af/GCF_016863015.1_ASM1686301v1_genomic.fna.gz | prodigal -d GCF_016863015.1_ASM1686301v1_genomic.fna/cds.fna -a GCF_016863015.1_ASM1686301v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:40,116] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:40,116] [INFO] Task started: HMMsearch
[2024-01-24 15:03:40,116] [INFO] Running command: hmmsearch --tblout GCF_016863015.1_ASM1686301v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d1fea62-81fe-4859-9af1-ea302dc21376/dqc_reference/reference_markers.hmm GCF_016863015.1_ASM1686301v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:40,549] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:40,550] [INFO] Found 6/6 markers.
[2024-01-24 15:03:40,617] [INFO] Query marker FASTA was written to GCF_016863015.1_ASM1686301v1_genomic.fna/markers.fasta
[2024-01-24 15:03:40,617] [INFO] Task started: Blastn
[2024-01-24 15:03:40,617] [INFO] Running command: blastn -query GCF_016863015.1_ASM1686301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d1fea62-81fe-4859-9af1-ea302dc21376/dqc_reference/reference_markers.fasta -out GCF_016863015.1_ASM1686301v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:42,018] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:42,021] [INFO] Selected 16 target genomes.
[2024-01-24 15:03:42,022] [INFO] Target genome list was writen to GCF_016863015.1_ASM1686301v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:42,028] [INFO] Task started: fastANI
[2024-01-24 15:03:42,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b224a73-4c20-4080-9fa7-e799c156e3af/GCF_016863015.1_ASM1686301v1_genomic.fna.gz --refList GCF_016863015.1_ASM1686301v1_genomic.fna/target_genomes.txt --output GCF_016863015.1_ASM1686301v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:04:16,024] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:16,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d1fea62-81fe-4859-9af1-ea302dc21376/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:04:16,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d1fea62-81fe-4859-9af1-ea302dc21376/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:04:16,037] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:04:16,037] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:04:16,037] [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 amethystogenes	strain=NBRC 101907	GCA_016863015.1	1427754	1427754	type	True	100.0	2639	2641	95	inconclusive
Microbispora cellulosiformans	strain=Gxj-6	GCA_008728085.1	2614688	2614688	type	True	97.4292	2398	2641	95	inconclusive
Microbispora fusca	strain=NEAU-HEGS1-5	GCA_005864065.1	2576905	2576905	type	True	94.4868	2186	2641	95	below_threshold
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	87.8845	1949	2641	95	below_threshold
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	87.7824	1909	2641	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	87.7382	1909	2641	95	below_threshold
Microbispora bryophytorum	strain=DSM 46710	GCA_006874465.1	1460882	1460882	type	True	87.4172	1821	2641	95	below_threshold
Microbispora camponoti	strain=2C-HV3	GCA_014712745.1	1677852	1677852	type	True	87.3572	1820	2641	95	below_threshold
Microbispora hainanensis	strain=DSM 45428	GCA_006874475.1	568844	568844	type	True	87.2676	1822	2641	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	86.7834	1620	2641	95	below_threshold
Microbispora rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	86.7744	1624	2641	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	83.1	1494	2641	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	82.0961	1141	2641	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.7503	832	2641	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.3521	1258	2641	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	78.8391	1171	2641	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:04:16,039] [INFO] DFAST Taxonomy check result was written to GCF_016863015.1_ASM1686301v1_genomic.fna/tc_result.tsv
[2024-01-24 15:04:16,040] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:04:16,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:04:16,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d1fea62-81fe-4859-9af1-ea302dc21376/dqc_reference/checkm_data
[2024-01-24 15:04:16,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:04:16,119] [INFO] Task started: CheckM
[2024-01-24 15:04:16,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863015.1_ASM1686301v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863015.1_ASM1686301v1_genomic.fna/checkm_input GCF_016863015.1_ASM1686301v1_genomic.fna/checkm_result
[2024-01-24 15:05:30,087] [INFO] Task succeeded: CheckM
[2024-01-24 15:05:30,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:05:30,111] [INFO] ===== Completeness check finished =====
[2024-01-24 15:05:30,111] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:05:30,112] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863015.1_ASM1686301v1_genomic.fna/markers.fasta)
[2024-01-24 15:05:30,112] [INFO] Task started: Blastn
[2024-01-24 15:05:30,112] [INFO] Running command: blastn -query GCF_016863015.1_ASM1686301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d1fea62-81fe-4859-9af1-ea302dc21376/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863015.1_ASM1686301v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:32,223] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:32,227] [INFO] Selected 11 target genomes.
[2024-01-24 15:05:32,227] [INFO] Target genome list was writen to GCF_016863015.1_ASM1686301v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:32,236] [INFO] Task started: fastANI
[2024-01-24 15:05:32,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b224a73-4c20-4080-9fa7-e799c156e3af/GCF_016863015.1_ASM1686301v1_genomic.fna.gz --refList GCF_016863015.1_ASM1686301v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863015.1_ASM1686301v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:56,360] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:56,375] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:56,375] [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	100.0	2639	2641	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	94.3177	2102	2641	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	87.93	1941	2641	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	87.7871	1913	2641	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	87.7326	1910	2641	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.99	95.83	0.88	0.87	3	-
GCF_900156315.1	s__Microbispora rosea	87.477	1889	2641	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	87.4001	1824	2641	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	87.2255	1828	2641	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	87.0755	1770	2641	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	86.7132	1635	2641	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	81.2445	1355	2641	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 15:05:56,377] [INFO] GTDB search result was written to GCF_016863015.1_ASM1686301v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:56,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:56,381] [INFO] DFAST_QC result json was written to GCF_016863015.1_ASM1686301v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:56,381] [INFO] DFAST_QC completed!
[2024-01-24 15:05:56,381] [INFO] Total running time: 0h2m41s