[2024-01-24 12:23:02,952] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:02,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:02,953] [INFO] DQC Reference Directory: /var/lib/cwl/stgaeb6564d-df6c-4f58-9f52-65dc083c6046/dqc_reference
[2024-01-24 12:23:04,115] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:04,115] [INFO] Task started: Prodigal
[2024-01-24 12:23:04,117] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9f3b597-45e6-4f38-bca7-965da8941107/GCF_014712735.1_ASM1471273v1_genomic.fna.gz | prodigal -d GCF_014712735.1_ASM1471273v1_genomic.fna/cds.fna -a GCF_014712735.1_ASM1471273v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:23,214] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:23,215] [INFO] Task started: HMMsearch
[2024-01-24 12:23:23,215] [INFO] Running command: hmmsearch --tblout GCF_014712735.1_ASM1471273v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaeb6564d-df6c-4f58-9f52-65dc083c6046/dqc_reference/reference_markers.hmm GCF_014712735.1_ASM1471273v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:23,507] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:23,508] [INFO] Found 6/6 markers.
[2024-01-24 12:23:23,563] [INFO] Query marker FASTA was written to GCF_014712735.1_ASM1471273v1_genomic.fna/markers.fasta
[2024-01-24 12:23:23,563] [INFO] Task started: Blastn
[2024-01-24 12:23:23,563] [INFO] Running command: blastn -query GCF_014712735.1_ASM1471273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeb6564d-df6c-4f58-9f52-65dc083c6046/dqc_reference/reference_markers.fasta -out GCF_014712735.1_ASM1471273v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:24,831] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:24,834] [INFO] Selected 13 target genomes.
[2024-01-24 12:23:24,834] [INFO] Target genome list was writen to GCF_014712735.1_ASM1471273v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:24,838] [INFO] Task started: fastANI
[2024-01-24 12:23:24,838] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9f3b597-45e6-4f38-bca7-965da8941107/GCF_014712735.1_ASM1471273v1_genomic.fna.gz --refList GCF_014712735.1_ASM1471273v1_genomic.fna/target_genomes.txt --output GCF_014712735.1_ASM1471273v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:52,387] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:52,387] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaeb6564d-df6c-4f58-9f52-65dc083c6046/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:52,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaeb6564d-df6c-4f58-9f52-65dc083c6046/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:52,396] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:23:52,396] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:23:52,396] [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 bryophytorum	strain=NEAU-TX2-2	GCA_014712735.1	1460882	1460882	type	True	100.0	2568	2573	95	inconclusive
Microbispora bryophytorum	strain=CGMCC 4.7138	GCA_014645855.1	1460882	1460882	type	True	99.9969	2559	2573	95	inconclusive
Microbispora bryophytorum	strain=DSM 46710	GCA_006874465.1	1460882	1460882	type	True	99.9952	2560	2573	95	inconclusive
Microbispora camponoti	strain=2C-HV3	GCA_014712745.1	1677852	1677852	type	True	97.6619	2354	2573	95	inconclusive
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	93.8766	2151	2573	95	below_threshold
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	93.1819	2227	2573	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	92.7301	2055	2573	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	83.1712	1507	2573	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	82.2192	1131	2573	95	below_threshold
Microtetraspora malaysiensis	strain=NBRC 100735	GCA_001528665.1	161358	161358	type	True	81.4045	1327	2573	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.8667	833	2573	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.4529	1287	2573	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	79.1366	1286	2573	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:52,398] [INFO] DFAST Taxonomy check result was written to GCF_014712735.1_ASM1471273v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:52,398] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:52,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:52,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaeb6564d-df6c-4f58-9f52-65dc083c6046/dqc_reference/checkm_data
[2024-01-24 12:23:52,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:52,468] [INFO] Task started: CheckM
[2024-01-24 12:23:52,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014712735.1_ASM1471273v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014712735.1_ASM1471273v1_genomic.fna/checkm_input GCF_014712735.1_ASM1471273v1_genomic.fna/checkm_result
[2024-01-24 12:24:57,998] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:57,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:58,020] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:58,020] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:58,021] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014712735.1_ASM1471273v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:58,021] [INFO] Task started: Blastn
[2024-01-24 12:24:58,021] [INFO] Running command: blastn -query GCF_014712735.1_ASM1471273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeb6564d-df6c-4f58-9f52-65dc083c6046/dqc_reference/reference_markers_gtdb.fasta -out GCF_014712735.1_ASM1471273v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:59,999] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:00,002] [INFO] Selected 11 target genomes.
[2024-01-24 12:25:00,002] [INFO] Target genome list was writen to GCF_014712735.1_ASM1471273v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:00,007] [INFO] Task started: fastANI
[2024-01-24 12:25:00,007] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9f3b597-45e6-4f38-bca7-965da8941107/GCF_014712735.1_ASM1471273v1_genomic.fna.gz --refList GCF_014712735.1_ASM1471273v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014712735.1_ASM1471273v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:25,018] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:25,026] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:25,027] [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	99.9952	2560	2573	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	93.8764	2151	2573	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	93.1313	2267	2573	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	92.7009	2059	2573	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	92.1464	2143	2573	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	91.0443	2043	2573	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	89.7314	1764	2573	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	81.4221	1338	2573	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	81.3932	1330	2573	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	79.8776	1228	2573	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	79.4124	1297	2573	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 12:25:25,028] [INFO] GTDB search result was written to GCF_014712735.1_ASM1471273v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:25,028] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:25,031] [INFO] DFAST_QC result json was written to GCF_014712735.1_ASM1471273v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:25,031] [INFO] DFAST_QC completed!
[2024-01-24 12:25:25,031] [INFO] Total running time: 0h2m22s