[2024-01-24 14:47:07,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:07,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:07,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b38625b-2870-431c-8f81-c91d1a1587ed/dqc_reference
[2024-01-24 14:47:08,979] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:08,986] [INFO] Task started: Prodigal
[2024-01-24 14:47:08,987] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ae166d8-690e-4b00-bdcf-ccb95971ca9a/GCF_014712745.1_ASM1471274v1_genomic.fna.gz | prodigal -d GCF_014712745.1_ASM1471274v1_genomic.fna/cds.fna -a GCF_014712745.1_ASM1471274v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:31,132] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:31,133] [INFO] Task started: HMMsearch
[2024-01-24 14:47:31,133] [INFO] Running command: hmmsearch --tblout GCF_014712745.1_ASM1471274v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b38625b-2870-431c-8f81-c91d1a1587ed/dqc_reference/reference_markers.hmm GCF_014712745.1_ASM1471274v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:31,564] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:31,565] [INFO] Found 6/6 markers.
[2024-01-24 14:47:31,635] [INFO] Query marker FASTA was written to GCF_014712745.1_ASM1471274v1_genomic.fna/markers.fasta
[2024-01-24 14:47:31,635] [INFO] Task started: Blastn
[2024-01-24 14:47:31,636] [INFO] Running command: blastn -query GCF_014712745.1_ASM1471274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b38625b-2870-431c-8f81-c91d1a1587ed/dqc_reference/reference_markers.fasta -out GCF_014712745.1_ASM1471274v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:33,102] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:33,105] [INFO] Selected 13 target genomes.
[2024-01-24 14:47:33,105] [INFO] Target genome list was writen to GCF_014712745.1_ASM1471274v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:33,110] [INFO] Task started: fastANI
[2024-01-24 14:47:33,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ae166d8-690e-4b00-bdcf-ccb95971ca9a/GCF_014712745.1_ASM1471274v1_genomic.fna.gz --refList GCF_014712745.1_ASM1471274v1_genomic.fna/target_genomes.txt --output GCF_014712745.1_ASM1471274v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:02,166] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:02,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b38625b-2870-431c-8f81-c91d1a1587ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:02,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b38625b-2870-431c-8f81-c91d1a1587ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:02,178] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:48:02,178] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:48:02,178] [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 camponoti	strain=2C-HV3	GCA_014712745.1	1677852	1677852	type	True	100.0	2619	2623	95	inconclusive
Microbispora bryophytorum	strain=CGMCC 4.7138	GCA_014645855.1	1460882	1460882	type	True	97.6125	2360	2623	95	inconclusive
Microbispora bryophytorum	strain=DSM 46710	GCA_006874465.1	1460882	1460882	type	True	97.6087	2350	2623	95	inconclusive
Microbispora bryophytorum	strain=NEAU-TX2-2	GCA_014712735.1	1460882	1460882	type	True	97.6045	2354	2623	95	inconclusive
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	93.788	2180	2623	95	below_threshold
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	93.065	2242	2623	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	92.6321	2079	2623	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	83.141	1512	2623	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	82.3544	1114	2623	95	below_threshold
Microtetraspora malaysiensis	strain=NBRC 100735	GCA_001528665.1	161358	161358	type	True	81.1537	1376	2623	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.8409	1320	2623	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.824	836	2623	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.5024	1285	2623	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:02,186] [INFO] DFAST Taxonomy check result was written to GCF_014712745.1_ASM1471274v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:02,187] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:02,187] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:02,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b38625b-2870-431c-8f81-c91d1a1587ed/dqc_reference/checkm_data
[2024-01-24 14:48:02,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:02,265] [INFO] Task started: CheckM
[2024-01-24 14:48:02,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014712745.1_ASM1471274v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014712745.1_ASM1471274v1_genomic.fna/checkm_input GCF_014712745.1_ASM1471274v1_genomic.fna/checkm_result
[2024-01-24 14:49:13,757] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:13,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:13,782] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:13,782] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:13,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014712745.1_ASM1471274v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:13,783] [INFO] Task started: Blastn
[2024-01-24 14:49:13,783] [INFO] Running command: blastn -query GCF_014712745.1_ASM1471274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b38625b-2870-431c-8f81-c91d1a1587ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_014712745.1_ASM1471274v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:15,983] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:15,986] [INFO] Selected 11 target genomes.
[2024-01-24 14:49:15,986] [INFO] Target genome list was writen to GCF_014712745.1_ASM1471274v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:15,994] [INFO] Task started: fastANI
[2024-01-24 14:49:15,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ae166d8-690e-4b00-bdcf-ccb95971ca9a/GCF_014712745.1_ASM1471274v1_genomic.fna.gz --refList GCF_014712745.1_ASM1471274v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014712745.1_ASM1471274v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:43,509] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:43,523] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:43,523] [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_006874465.1	s__Microbispora bryophytorum	97.5988	2351	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.22	97.66	0.97	0.91	4	conclusive
GCF_006334915.2	s__Microbispora catharanthi	93.7792	2181	2623	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	93.0159	2273	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.16	98.33	0.97	0.94	3	-
GCF_016863095.1	s__Microbispora siamensis	92.6141	2081	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.99	95.83	0.88	0.87	3	-
GCF_006874475.1	s__Microbispora hainanensis	92.0605	2153	2623	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	91.0872	2047	2623	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	89.7495	1757	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001570385.1	s__Microtetraspora glauca	81.3867	1371	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001528665.1	s__Microtetraspora malaysiensis	81.1683	1374	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109355.1	s__Nonomuraea pusilla	79.7922	1235	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.44	99.44	0.97	0.97	2	-
GCF_900099965.1	s__Nonomuraea jiangxiensis	79.2571	1290	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:43,527] [INFO] GTDB search result was written to GCF_014712745.1_ASM1471274v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:43,527] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:43,535] [INFO] DFAST_QC result json was written to GCF_014712745.1_ASM1471274v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:43,536] [INFO] DFAST_QC completed!
[2024-01-24 14:49:43,536] [INFO] Total running time: 0h2m36s