[2024-01-24 12:29:19,331] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:19,333] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:19,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg98ac9d42-b196-4a7b-a5b5-d68f63a189c0/dqc_reference
[2024-01-24 12:29:20,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:20,523] [INFO] Task started: Prodigal
[2024-01-24 12:29:20,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg43a56380-fc00-4f5d-8433-875f9434ab6d/GCF_027921885.1_ASM2792188v1_genomic.fna.gz | prodigal -d GCF_027921885.1_ASM2792188v1_genomic.fna/cds.fna -a GCF_027921885.1_ASM2792188v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:38,618] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:38,619] [INFO] Task started: HMMsearch
[2024-01-24 12:29:38,619] [INFO] Running command: hmmsearch --tblout GCF_027921885.1_ASM2792188v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98ac9d42-b196-4a7b-a5b5-d68f63a189c0/dqc_reference/reference_markers.hmm GCF_027921885.1_ASM2792188v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:38,977] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:38,979] [INFO] Found 6/6 markers.
[2024-01-24 12:29:39,035] [INFO] Query marker FASTA was written to GCF_027921885.1_ASM2792188v1_genomic.fna/markers.fasta
[2024-01-24 12:29:39,036] [INFO] Task started: Blastn
[2024-01-24 12:29:39,036] [INFO] Running command: blastn -query GCF_027921885.1_ASM2792188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98ac9d42-b196-4a7b-a5b5-d68f63a189c0/dqc_reference/reference_markers.fasta -out GCF_027921885.1_ASM2792188v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:40,414] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:40,419] [INFO] Selected 14 target genomes.
[2024-01-24 12:29:40,420] [INFO] Target genome list was writen to GCF_027921885.1_ASM2792188v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:40,440] [INFO] Task started: fastANI
[2024-01-24 12:29:40,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg43a56380-fc00-4f5d-8433-875f9434ab6d/GCF_027921885.1_ASM2792188v1_genomic.fna.gz --refList GCF_027921885.1_ASM2792188v1_genomic.fna/target_genomes.txt --output GCF_027921885.1_ASM2792188v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:07,635] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:07,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98ac9d42-b196-4a7b-a5b5-d68f63a189c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:07,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98ac9d42-b196-4a7b-a5b5-d68f63a189c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:07,652] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:30:07,652] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:07,653] [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 rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	99.9894	2208	2215	95	conclusive
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	99.9746	2162	2215	95	conclusive
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	90.7477	1759	2215	95	below_threshold
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	90.6283	1789	2215	95	below_threshold
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	90.5187	1772	2215	95	below_threshold
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	90.2099	1738	2215	95	below_threshold
Microbispora hainanensis	strain=DSM 45428	GCA_006874475.1	568844	568844	type	True	90.2061	1784	2215	95	below_threshold
Microbispora cellulosiformans	strain=Gxj-6	GCA_008728085.1	2614688	2614688	type	True	86.9168	1597	2215	95	below_threshold
Microbispora amethystogenes	strain=NBRC 101907	GCA_016863015.1	1427754	1427754	type	True	86.9102	1579	2215	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	82.7463	1309	2215	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	82.4512	1069	2215	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	80.062	1162	2215	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.0269	1165	2215	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.9588	803	2215	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:07,654] [INFO] DFAST Taxonomy check result was written to GCF_027921885.1_ASM2792188v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:07,655] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:07,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:07,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98ac9d42-b196-4a7b-a5b5-d68f63a189c0/dqc_reference/checkm_data
[2024-01-24 12:30:07,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:07,730] [INFO] Task started: CheckM
[2024-01-24 12:30:07,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027921885.1_ASM2792188v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027921885.1_ASM2792188v1_genomic.fna/checkm_input GCF_027921885.1_ASM2792188v1_genomic.fna/checkm_result
[2024-01-24 12:31:03,664] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:03,666] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:03,687] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:03,688] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:03,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027921885.1_ASM2792188v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:03,689] [INFO] Task started: Blastn
[2024-01-24 12:31:03,689] [INFO] Running command: blastn -query GCF_027921885.1_ASM2792188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98ac9d42-b196-4a7b-a5b5-d68f63a189c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_027921885.1_ASM2792188v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:06,005] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:06,009] [INFO] Selected 10 target genomes.
[2024-01-24 12:31:06,009] [INFO] Target genome list was writen to GCF_027921885.1_ASM2792188v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:06,020] [INFO] Task started: fastANI
[2024-01-24 12:31:06,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg43a56380-fc00-4f5d-8433-875f9434ab6d/GCF_027921885.1_ASM2792188v1_genomic.fna.gz --refList GCF_027921885.1_ASM2792188v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027921885.1_ASM2792188v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:27,787] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:27,796] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:27,797] [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_014647835.1	s__Microbispora aerata	99.9894	2208	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016863095.1	s__Microbispora siamensis	90.7044	1766	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	96.99	95.83	0.88	0.87	3	-
GCF_006334915.2	s__Microbispora catharanthi	90.5433	1768	2215	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	90.2712	1782	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	98.71	98.71	0.93	0.93	2	-
GCF_006874475.1	s__Microbispora hainanensis	90.1981	1785	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	95.41	95.40	0.85	0.85	4	-
GCF_900156315.1	s__Microbispora rosea	90.1561	1772	2215	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	89.8769	1714	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	99.22	97.66	0.97	0.91	4	-
GCF_012999535.1	s__Microbispora sp012999535	89.1308	1671	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863015.1	s__Microbispora amethystogenes	86.9412	1574	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.43	97.43	0.91	0.91	2	-
GCF_001570365.1	s__Microtetraspora fusca	81.3738	1262	2215	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 12:31:27,798] [INFO] GTDB search result was written to GCF_027921885.1_ASM2792188v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:27,799] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:27,803] [INFO] DFAST_QC result json was written to GCF_027921885.1_ASM2792188v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:27,803] [INFO] DFAST_QC completed!
[2024-01-24 12:31:27,803] [INFO] Total running time: 0h2m8s