[2024-01-24 13:24:12,353] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:12,354] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:12,355] [INFO] DQC Reference Directory: /var/lib/cwl/stg82e941f6-083d-4a61-9703-66b22704429b/dqc_reference
[2024-01-24 13:24:13,534] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:13,535] [INFO] Task started: Prodigal
[2024-01-24 13:24:13,535] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6e1e9ef-81f8-465e-976c-f56c5255f60b/GCF_014191605.1_ASM1419160v1_genomic.fna.gz | prodigal -d GCF_014191605.1_ASM1419160v1_genomic.fna/cds.fna -a GCF_014191605.1_ASM1419160v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:28,419] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:28,419] [INFO] Task started: HMMsearch
[2024-01-24 13:24:28,419] [INFO] Running command: hmmsearch --tblout GCF_014191605.1_ASM1419160v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82e941f6-083d-4a61-9703-66b22704429b/dqc_reference/reference_markers.hmm GCF_014191605.1_ASM1419160v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:28,654] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:28,656] [INFO] Found 6/6 markers.
[2024-01-24 13:24:28,695] [INFO] Query marker FASTA was written to GCF_014191605.1_ASM1419160v1_genomic.fna/markers.fasta
[2024-01-24 13:24:28,696] [INFO] Task started: Blastn
[2024-01-24 13:24:28,696] [INFO] Running command: blastn -query GCF_014191605.1_ASM1419160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82e941f6-083d-4a61-9703-66b22704429b/dqc_reference/reference_markers.fasta -out GCF_014191605.1_ASM1419160v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:29,962] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:29,966] [INFO] Selected 18 target genomes.
[2024-01-24 13:24:29,966] [INFO] Target genome list was writen to GCF_014191605.1_ASM1419160v1_genomic.fna/target_genomes.txt
[2024-01-24 13:24:29,983] [INFO] Task started: fastANI
[2024-01-24 13:24:29,983] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6e1e9ef-81f8-465e-976c-f56c5255f60b/GCF_014191605.1_ASM1419160v1_genomic.fna.gz --refList GCF_014191605.1_ASM1419160v1_genomic.fna/target_genomes.txt --output GCF_014191605.1_ASM1419160v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:24:53,999] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:54,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82e941f6-083d-4a61-9703-66b22704429b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:24:54,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82e941f6-083d-4a61-9703-66b22704429b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:24:54,014] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:24:54,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:24:54,015] [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
Prauserella isguenensis	strain=CECT 8577	GCA_014191605.1	1470180	1470180	type	True	100.0	1643	1643	95	conclusive
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	92.9567	1429	1643	95	below_threshold
Prauserella rugosa	strain=NRRL B-2295	GCA_000719975.1	43354	43354	type	True	84.3205	1263	1643	95	below_threshold
Prauserella rugosa	strain=DSM 43194	GCA_007829565.1	43354	43354	type	True	84.2444	1283	1643	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	80.3294	938	1643	95	below_threshold
Saccharomonospora iraqiensis subsp. paurometabolica	strain=YIM 90007	GCA_000231035.3	208085	52698	type	True	79.4637	651	1643	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.3825	820	1643	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	79.3394	737	1643	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	79.2659	770	1643	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	79.2143	774	1643	95	below_threshold
Amycolatopsis albispora	strain=WP1	GCA_003312875.1	1804986	1804986	type	True	79.0271	804	1643	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	78.975	782	1643	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.9259	787	1643	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	78.6802	808	1643	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	77.9177	628	1643	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	77.8179	652	1643	95	below_threshold
Actinokineospora bangkokensis	strain=44EHW	GCA_001940455.1	1193682	1193682	type	True	77.7846	622	1643	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	77.7021	652	1643	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:24:54,016] [INFO] DFAST Taxonomy check result was written to GCF_014191605.1_ASM1419160v1_genomic.fna/tc_result.tsv
[2024-01-24 13:24:54,017] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:24:54,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:24:54,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82e941f6-083d-4a61-9703-66b22704429b/dqc_reference/checkm_data
[2024-01-24 13:24:54,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:24:54,063] [INFO] Task started: CheckM
[2024-01-24 13:24:54,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191605.1_ASM1419160v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191605.1_ASM1419160v1_genomic.fna/checkm_input GCF_014191605.1_ASM1419160v1_genomic.fna/checkm_result
[2024-01-24 13:26:09,076] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:09,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:09,101] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:09,101] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:09,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191605.1_ASM1419160v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:09,102] [INFO] Task started: Blastn
[2024-01-24 13:26:09,102] [INFO] Running command: blastn -query GCF_014191605.1_ASM1419160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82e941f6-083d-4a61-9703-66b22704429b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191605.1_ASM1419160v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:11,015] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:11,018] [INFO] Selected 15 target genomes.
[2024-01-24 13:26:11,018] [INFO] Target genome list was writen to GCF_014191605.1_ASM1419160v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:11,042] [INFO] Task started: fastANI
[2024-01-24 13:26:11,042] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6e1e9ef-81f8-465e-976c-f56c5255f60b/GCF_014191605.1_ASM1419160v1_genomic.fna.gz --refList GCF_014191605.1_ASM1419160v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191605.1_ASM1419160v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:33,057] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:33,069] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:33,070] [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_014191605.1	s__Saccharomonospora isguenensis	100.0	1643	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014195435.1	s__Saccharomonospora sediminis	88.8727	1406	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719975.1	s__Saccharomonospora rugosa	84.3305	1261	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.54	99.08	0.98	0.95	3	-
GCF_001942305.1	s__Saccharomonospora sp001942305	83.6684	1123	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202235.1	s__Saccharomonospora sp003202235	80.5803	962	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005146945.1	s__Saccharomonospora endophytica	80.356	942	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	-
GCF_016595675.1	s__Saccharomonospora sp016595675	80.3352	937	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001955.1	s__Saccharomonospora shujinwangii	80.1321	857	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739085.1	s__Amycolatopsis methanolica	79.3343	831	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	100.00	100.00	1.00	1.00	2	-
GCF_009765355.1	s__Amycolatopsis anabasis	78.9413	789	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902497555.1	s__Amycolatopsis sp902497555	78.8828	795	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105945.1	s__Amycolatopsis tolypomycina	78.6777	805	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014735.1	s__Actinosynnema carneum	77.9231	627	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_006716745.1	s__Actinosynnema saharense	77.7799	659	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752005.1	s__Actinosynnema texasense	77.6852	656	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:33,071] [INFO] GTDB search result was written to GCF_014191605.1_ASM1419160v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:33,072] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:33,076] [INFO] DFAST_QC result json was written to GCF_014191605.1_ASM1419160v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:33,076] [INFO] DFAST_QC completed!
[2024-01-24 13:26:33,076] [INFO] Total running time: 0h2m21s