[2024-01-24 13:33:40,903] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:40,908] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:40,909] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5664e03-574d-4e54-acf0-f2efa7a5dd5f/dqc_reference
[2024-01-24 13:33:42,285] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:42,286] [INFO] Task started: Prodigal
[2024-01-24 13:33:42,286] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa9739a1-b05e-43e5-bc3f-6467c45923de/GCF_000737315.1_ASM73731v1_genomic.fna.gz | prodigal -d GCF_000737315.1_ASM73731v1_genomic.fna/cds.fna -a GCF_000737315.1_ASM73731v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:34:23,030] [INFO] Task succeeded: Prodigal
[2024-01-24 13:34:23,031] [INFO] Task started: HMMsearch
[2024-01-24 13:34:23,031] [INFO] Running command: hmmsearch --tblout GCF_000737315.1_ASM73731v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5664e03-574d-4e54-acf0-f2efa7a5dd5f/dqc_reference/reference_markers.hmm GCF_000737315.1_ASM73731v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:34:23,461] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:34:23,463] [INFO] Found 6/6 markers.
[2024-01-24 13:34:23,553] [INFO] Query marker FASTA was written to GCF_000737315.1_ASM73731v1_genomic.fna/markers.fasta
[2024-01-24 13:34:23,554] [INFO] Task started: Blastn
[2024-01-24 13:34:23,554] [INFO] Running command: blastn -query GCF_000737315.1_ASM73731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5664e03-574d-4e54-acf0-f2efa7a5dd5f/dqc_reference/reference_markers.fasta -out GCF_000737315.1_ASM73731v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:24,349] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:24,353] [INFO] Selected 20 target genomes.
[2024-01-24 13:34:24,354] [INFO] Target genome list was writen to GCF_000737315.1_ASM73731v1_genomic.fna/target_genomes.txt
[2024-01-24 13:34:24,393] [INFO] Task started: fastANI
[2024-01-24 13:34:24,393] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa9739a1-b05e-43e5-bc3f-6467c45923de/GCF_000737315.1_ASM73731v1_genomic.fna.gz --refList GCF_000737315.1_ASM73731v1_genomic.fna/target_genomes.txt --output GCF_000737315.1_ASM73731v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:34:56,795] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:56,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5664e03-574d-4e54-acf0-f2efa7a5dd5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:34:56,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5664e03-574d-4e54-acf0-f2efa7a5dd5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:34:56,812] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:34:56,812] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:34:56,812] [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
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	82.4719	1816	3707	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	82.3932	1817	3707	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	82.3699	1795	3707	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	80.5291	1755	3707	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	80.5227	1746	3707	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	80.5186	1746	3707	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	80.4706	1759	3707	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	80.3943	1668	3707	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	80.3074	1415	3707	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	80.1335	1496	3707	95	below_threshold
Corallococcus carmarthensis	strain=CA043D	GCA_003611695.1	2316728	2316728	type	True	80.1	1423	3707	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	75.1416	77	3707	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.1115	241	3707	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.0881	242	3707	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.0802	228	3707	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.0366	245	3707	95	below_threshold
Nesterenkonia lacusekhoensis	strain=DSM 12544	GCA_017876395.1	150832	150832	type	True	75.0108	72	3707	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	74.8767	215	3707	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:34:56,814] [INFO] DFAST Taxonomy check result was written to GCF_000737315.1_ASM73731v1_genomic.fna/tc_result.tsv
[2024-01-24 13:34:56,815] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:34:56,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:34:56,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5664e03-574d-4e54-acf0-f2efa7a5dd5f/dqc_reference/checkm_data
[2024-01-24 13:34:56,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:34:56,916] [INFO] Task started: CheckM
[2024-01-24 13:34:56,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000737315.1_ASM73731v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000737315.1_ASM73731v1_genomic.fna/checkm_input GCF_000737315.1_ASM73731v1_genomic.fna/checkm_result
[2024-01-24 13:37:28,720] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:28,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:28,743] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:28,744] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:28,744] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000737315.1_ASM73731v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:28,744] [INFO] Task started: Blastn
[2024-01-24 13:37:28,745] [INFO] Running command: blastn -query GCF_000737315.1_ASM73731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5664e03-574d-4e54-acf0-f2efa7a5dd5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000737315.1_ASM73731v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:30,168] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:30,173] [INFO] Selected 12 target genomes.
[2024-01-24 13:37:30,173] [INFO] Target genome list was writen to GCF_000737315.1_ASM73731v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:30,186] [INFO] Task started: fastANI
[2024-01-24 13:37:30,186] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa9739a1-b05e-43e5-bc3f-6467c45923de/GCF_000737315.1_ASM73731v1_genomic.fna.gz --refList GCF_000737315.1_ASM73731v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000737315.1_ASM73731v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:04,781] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:04,802] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:04,802] [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_000737315.1	s__Hyalangium minutum	100.0	3679	3707	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Hyalangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016926755.1	s__Hyalangium sp016926755	84.704	1990	3707	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Hyalangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111745.1	s__Stigmatella erecta	82.4836	1812	3707	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.281	N/A	N/A	N/A	N/A	1	-
GCF_900109545.1	s__Stigmatella aurantiaca	82.4076	1814	3707	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.281	N/A	N/A	N/A	N/A	1	-
GCF_000165485.1	s__Stigmatella aurantiaca_A	81.6586	1792	3707	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010894435.1	s__Myxococcus trucidator	80.5166	1748	3707	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027285.1	s__Archangium gephyra	80.4741	1755	3707	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016887565.1	s__Archangium violaceum_B	80.4583	1730	3707	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016859125.1	s__Archangium violaceum_A	80.4402	1651	3707	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733295.1	s__Archangium violaceum	80.4035	1664	3707	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	95.60	95.60	0.86	0.86	2	-
GCF_009909145.1	s__Corallococcus sp009909145	80.3088	1416	3707	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	99.47	99.47	0.98	0.98	2	-
GCF_002305875.1	s__Cystobacter fuscus_A	80.1543	1529	3707	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Cystobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:04,804] [INFO] GTDB search result was written to GCF_000737315.1_ASM73731v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:04,805] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:04,809] [INFO] DFAST_QC result json was written to GCF_000737315.1_ASM73731v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:04,809] [INFO] DFAST_QC completed!
[2024-01-24 13:38:04,809] [INFO] Total running time: 0h4m24s