[2024-01-24 14:42:02,780] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:42:02,782] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:42:02,783] [INFO] DQC Reference Directory: /var/lib/cwl/stg32645242-bd2e-4214-9d15-79fc60638f8d/dqc_reference
[2024-01-24 14:42:04,126] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:42:04,127] [INFO] Task started: Prodigal
[2024-01-24 14:42:04,128] [INFO] Running command: gunzip -c /var/lib/cwl/stg99cd1d31-5d56-4f85-a813-b971d67f3ec9/GCF_016863035.1_ASM1686303v1_genomic.fna.gz | prodigal -d GCF_016863035.1_ASM1686303v1_genomic.fna/cds.fna -a GCF_016863035.1_ASM1686303v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:42:28,139] [INFO] Task succeeded: Prodigal
[2024-01-24 14:42:28,140] [INFO] Task started: HMMsearch
[2024-01-24 14:42:28,140] [INFO] Running command: hmmsearch --tblout GCF_016863035.1_ASM1686303v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32645242-bd2e-4214-9d15-79fc60638f8d/dqc_reference/reference_markers.hmm GCF_016863035.1_ASM1686303v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:42:28,522] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:42:28,524] [INFO] Found 6/6 markers.
[2024-01-24 14:42:28,597] [INFO] Query marker FASTA was written to GCF_016863035.1_ASM1686303v1_genomic.fna/markers.fasta
[2024-01-24 14:42:28,597] [INFO] Task started: Blastn
[2024-01-24 14:42:28,597] [INFO] Running command: blastn -query GCF_016863035.1_ASM1686303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32645242-bd2e-4214-9d15-79fc60638f8d/dqc_reference/reference_markers.fasta -out GCF_016863035.1_ASM1686303v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:29,981] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:29,985] [INFO] Selected 14 target genomes.
[2024-01-24 14:42:29,986] [INFO] Target genome list was writen to GCF_016863035.1_ASM1686303v1_genomic.fna/target_genomes.txt
[2024-01-24 14:42:29,992] [INFO] Task started: fastANI
[2024-01-24 14:42:29,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg99cd1d31-5d56-4f85-a813-b971d67f3ec9/GCF_016863035.1_ASM1686303v1_genomic.fna.gz --refList GCF_016863035.1_ASM1686303v1_genomic.fna/target_genomes.txt --output GCF_016863035.1_ASM1686303v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:42:58,761] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:58,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32645242-bd2e-4214-9d15-79fc60638f8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:42:58,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32645242-bd2e-4214-9d15-79fc60638f8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:42:58,778] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:42:58,778] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:42:58,778] [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 corallina	strain=NBRC 16416	GCA_016863035.1	83302	83302	type	True	100.0	2728	2732	95	conclusive
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	84.1561	1627	2732	95	below_threshold
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	84.0993	1776	2732	95	below_threshold
Microbispora rosea	strain=ATCC 12950	GCA_900156315.1	58117	58117	type	True	84.052	1813	2732	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	84.0009	1820	2732	95	below_threshold
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	83.9903	1823	2732	95	below_threshold
Microbispora hainanensis	strain=DSM 45428	GCA_006874475.1	568844	568844	type	True	83.9825	1769	2732	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	83.6037	1472	2732	95	below_threshold
Microbispora cellulosiformans	strain=Gxj-6	GCA_008728085.1	2614688	2614688	type	True	83.5323	1612	2732	95	below_threshold
Microbispora fusca	strain=NEAU-HEGS1-5	GCA_005864065.1	2576905	2576905	type	True	83.4837	1623	2732	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	82.2827	1125	2732	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.708	1376	2732	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.6851	880	2732	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.3511	1293	2732	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:42:58,780] [INFO] DFAST Taxonomy check result was written to GCF_016863035.1_ASM1686303v1_genomic.fna/tc_result.tsv
[2024-01-24 14:42:58,781] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:42:58,781] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:42:58,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32645242-bd2e-4214-9d15-79fc60638f8d/dqc_reference/checkm_data
[2024-01-24 14:42:58,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:42:58,858] [INFO] Task started: CheckM
[2024-01-24 14:42:58,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863035.1_ASM1686303v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863035.1_ASM1686303v1_genomic.fna/checkm_input GCF_016863035.1_ASM1686303v1_genomic.fna/checkm_result
[2024-01-24 14:44:38,902] [INFO] Task succeeded: CheckM
[2024-01-24 14:44:38,904] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 1.85%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2024-01-24 14:44:38,935] [INFO] ===== Completeness check finished =====
[2024-01-24 14:44:38,936] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:44:38,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863035.1_ASM1686303v1_genomic.fna/markers.fasta)
[2024-01-24 14:44:38,937] [INFO] Task started: Blastn
[2024-01-24 14:44:38,937] [INFO] Running command: blastn -query GCF_016863035.1_ASM1686303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32645242-bd2e-4214-9d15-79fc60638f8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863035.1_ASM1686303v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:44:41,205] [INFO] Task succeeded: Blastn
[2024-01-24 14:44:41,209] [INFO] Selected 14 target genomes.
[2024-01-24 14:44:41,209] [INFO] Target genome list was writen to GCF_016863035.1_ASM1686303v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:44:41,262] [INFO] Task started: fastANI
[2024-01-24 14:44:41,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg99cd1d31-5d56-4f85-a813-b971d67f3ec9/GCF_016863035.1_ASM1686303v1_genomic.fna.gz --refList GCF_016863035.1_ASM1686303v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863035.1_ASM1686303v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:45:11,086] [INFO] Task succeeded: fastANI
[2024-01-24 14:45:11,104] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:45:11,104] [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_016863035.1	s__Microbispora corallina	100.0	2728	2732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.01	97.01	0.91	0.91	2	conclusive
GCF_017896165.1	s__Microbispora sp017896165	84.1328	1631	2732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006334915.2	s__Microbispora catharanthi	84.1263	1828	2732	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	84.0559	1814	2732	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	84.011	1765	2732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	95.41	95.40	0.85	0.85	4	-
GCF_016863095.1	s__Microbispora siamensis	83.9952	1822	2732	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	83.8759	1696	2732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.22	97.66	0.97	0.91	4	-
GCF_014161445.1	s__Microbispora sp014161445	83.8425	1744	2732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.71	98.71	0.93	0.93	2	-
GCF_012999535.1	s__Microbispora sp012999535	83.6933	1596	2732	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	83.5907	1557	2732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.16	96.98	0.92	0.88	7	-
GCF_014647835.1	s__Microbispora aerata	83.5848	1471	2732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016863015.1	s__Microbispora amethystogenes	83.4931	1605	2732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.43	97.43	0.91	0.91	2	-
GCF_016863115.1	s__Sphaerimonospora thailandensis	82.3242	1118	2732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerimonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001552515.1	s__Sphaerimonospora mesophila	82.2102	1236	2732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerimonospora	95.0	99.25	99.25	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:45:11,106] [INFO] GTDB search result was written to GCF_016863035.1_ASM1686303v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:45:11,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:45:11,122] [INFO] DFAST_QC result json was written to GCF_016863035.1_ASM1686303v1_genomic.fna/dqc_result.json
[2024-01-24 14:45:11,122] [INFO] DFAST_QC completed!
[2024-01-24 14:45:11,123] [INFO] Total running time: 0h3m8s