[2024-01-24 12:31:33,898] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:33,901] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:33,901] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa481788-b238-49b1-babf-0f8a5f0267b2/dqc_reference
[2024-01-24 12:31:35,087] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,088] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,088] [INFO] Running command: gunzip -c /var/lib/cwl/stg99e0b5ed-207f-4e0e-b896-c09acbead327/GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/cds.fna -a GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:07,513] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:07,514] [INFO] Task started: HMMsearch
[2024-01-24 12:32:07,514] [INFO] Running command: hmmsearch --tblout GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa481788-b238-49b1-babf-0f8a5f0267b2/dqc_reference/reference_markers.hmm GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:07,896] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:07,898] [INFO] Found 6/6 markers.
[2024-01-24 12:32:07,965] [INFO] Query marker FASTA was written to GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:32:07,965] [INFO] Task started: Blastn
[2024-01-24 12:32:07,965] [INFO] Running command: blastn -query GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa481788-b238-49b1-babf-0f8a5f0267b2/dqc_reference/reference_markers.fasta -out GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:09,303] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:09,308] [INFO] Selected 24 target genomes.
[2024-01-24 12:32:09,308] [INFO] Target genome list was writen to GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:32:09,334] [INFO] Task started: fastANI
[2024-01-24 12:32:09,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg99e0b5ed-207f-4e0e-b896-c09acbead327/GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna.gz --refList GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:52,831] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:52,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa481788-b238-49b1-babf-0f8a5f0267b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:52,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa481788-b238-49b1-babf-0f8a5f0267b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:52,857] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:32:52,857] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:52,858] [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
Allokutzneria albata	strain=DSM 44149	GCA_900103775.1	211114	211114	type	True	100.0	2854	2855	95	conclusive
Allokutzneria albata	strain=NRRL B-24461	GCA_000720955.1	211114	211114	type	True	99.9721	2785	2855	95	conclusive
Crossiella equi	strain=NRRL B-24104	GCA_002155995.1	130796	130796	type	True	79.6766	1164	2855	95	below_threshold
Crossiella cryophila	strain=DSM 44230	GCA_014204915.1	43355	43355	type	True	79.6082	1272	2855	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	79.3027	1100	2855	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	79.267	910	2855	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	79.1293	976	2855	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	78.8417	1025	2855	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	78.8177	920	2855	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	78.8031	1096	2855	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	78.7048	1224	2855	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	78.683	975	2855	95	below_threshold
Actinokineospora bangkokensis	strain=44EHW	GCA_001940455.1	1193682	1193682	type	True	78.6715	994	2855	95	below_threshold
Actinosynnema mirum	strain=DSM 43827	GCA_000023245.1	40567	40567	type	True	78.628	1056	2855	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	78.627	1237	2855	95	below_threshold
Actinokineospora inagensis	strain=DSM 44258	GCA_000482865.1	103730	103730	type	True	78.5785	803	2855	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	78.5173	996	2855	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	78.5044	995	2855	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.4809	860	2855	95	below_threshold
Lentzea xinjiangensis	strain=CGMCC 4.3525	GCA_900110955.1	402600	402600	type	True	78.4056	1026	2855	95	below_threshold
Lentzea guizhouensis	strain=DHS C013	GCA_001701025.1	1586287	1586287	type	True	78.3743	1037	2855	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	78.3637	1002	2855	95	below_threshold
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	77.8635	740	2855	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.8427	1012	2855	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:52,859] [INFO] DFAST Taxonomy check result was written to GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:32:52,860] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:52,860] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:52,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa481788-b238-49b1-babf-0f8a5f0267b2/dqc_reference/checkm_data
[2024-01-24 12:32:52,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:52,936] [INFO] Task started: CheckM
[2024-01-24 12:32:52,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/checkm_input GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:35:28,882] [INFO] Task succeeded: CheckM
[2024-01-24 12:35:28,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:35:28,910] [INFO] ===== Completeness check finished =====
[2024-01-24 12:35:28,910] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:35:28,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:35:28,911] [INFO] Task started: Blastn
[2024-01-24 12:35:28,911] [INFO] Running command: blastn -query GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa481788-b238-49b1-babf-0f8a5f0267b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:35:31,025] [INFO] Task succeeded: Blastn
[2024-01-24 12:35:31,028] [INFO] Selected 21 target genomes.
[2024-01-24 12:35:31,029] [INFO] Target genome list was writen to GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:35:31,215] [INFO] Task started: fastANI
[2024-01-24 12:35:31,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg99e0b5ed-207f-4e0e-b896-c09acbead327/GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna.gz --refList GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:36:09,496] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:09,517] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:36:09,518] [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_900103775.1	s__Allokutzneria albata	100.0	2855	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Allokutzneria	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002155965.1	s__Allokutzneria sp002155965	88.6976	2043	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Allokutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876755.1	s__Crossiella equi	79.6543	1278	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014204915.1	s__Crossiella cryophila	79.5895	1270	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	79.1207	977	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464305.1	s__REN6 sp016464305	79.0893	924	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__REN6	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386585.1	s__AN110305 sp008386585	79.0477	1084	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__AN110305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634935.1	s__Actinosynnema australiense	78.817	1034	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014735.1	s__Actinosynnema carneum	78.8132	1040	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_003182415.1	s__Actinokineospora mzabensis	78.7426	965	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_001940455.1	s__Actinokineospora bangkokensis	78.6968	987	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498035.1	s__Actinosynnema syringae	78.6103	1244	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000482865.1	s__Actinokineospora inagensis	78.5982	800	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002815.1	s__Umezawaea tangerina	78.5972	1157	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Umezawaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023245.1	s__Actinosynnema mirum	78.5457	1068	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	96.4703	99.51	99.51	0.95	0.95	3	-
GCF_007845675.1	s__Lentzea sp007845675	78.503	999	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110955.1	s__Lentzea xinjiangensis	78.4363	1014	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279525.1	s__Lentzea sp001279525	78.3492	1064	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464705.1	s__Saccharomonospora sp016464705	77.9757	744	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016889705.1	s__Amycolatopsis sp016889705	77.6131	843	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070045.1	s__Micromonospora sp018070045	76.8707	612	2855	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:36:09,521] [INFO] GTDB search result was written to GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:36:09,521] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:36:09,526] [INFO] DFAST_QC result json was written to GCF_900103775.1_IMG-taxon_2634166198_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:36:09,526] [INFO] DFAST_QC completed!
[2024-01-24 12:36:09,526] [INFO] Total running time: 0h4m36s