[2024-01-24 14:05:00,031] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:00,033] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:00,034] [INFO] DQC Reference Directory: /var/lib/cwl/stg94aedeed-032f-4a41-a247-835671f3f0a8/dqc_reference
[2024-01-24 14:05:01,236] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:01,237] [INFO] Task started: Prodigal
[2024-01-24 14:05:01,237] [INFO] Running command: gunzip -c /var/lib/cwl/stg6daf27dd-63f1-4eec-8afb-8621468b346f/GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/cds.fna -a GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:35,112] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:35,113] [INFO] Task started: HMMsearch
[2024-01-24 14:05:35,113] [INFO] Running command: hmmsearch --tblout GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94aedeed-032f-4a41-a247-835671f3f0a8/dqc_reference/reference_markers.hmm GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:35,535] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:35,536] [INFO] Found 6/6 markers.
[2024-01-24 14:05:35,608] [INFO] Query marker FASTA was written to GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:05:35,608] [INFO] Task started: Blastn
[2024-01-24 14:05:35,608] [INFO] Running command: blastn -query GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg94aedeed-032f-4a41-a247-835671f3f0a8/dqc_reference/reference_markers.fasta -out GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:36,359] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:36,362] [INFO] Selected 21 target genomes.
[2024-01-24 14:05:36,362] [INFO] Target genome list was writen to GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:05:36,383] [INFO] Task started: fastANI
[2024-01-24 14:05:36,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg6daf27dd-63f1-4eec-8afb-8621468b346f/GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna.gz --refList GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:20,732] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:20,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94aedeed-032f-4a41-a247-835671f3f0a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:20,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94aedeed-032f-4a41-a247-835671f3f0a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:20,748] [INFO] Found 21 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:06:20,748] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:06:20,749] [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 aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	100.0	3087	3090	95	inconclusive
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	97.3718	2794	3090	95	inconclusive
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	95.26	2753	3090	95	inconclusive
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	80.9701	1543	3090	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	80.9327	1603	3090	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	80.9279	1598	3090	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	80.8834	1342	3090	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	80.8187	1239	3090	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	80.8187	1372	3090	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	80.7222	1620	3090	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	80.6973	1610	3090	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	80.6954	1497	3090	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	80.6162	1529	3090	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	80.5996	1425	3090	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	80.5636	1445	3090	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_900101365.1	381306	381306	type	True	75.3282	153	3090	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_001399755.1	381306	381306	type	True	75.3176	151	3090	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	75.2942	142	3090	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.2253	387	3090	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.1818	370	3090	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.0183	180	3090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:20,750] [INFO] DFAST Taxonomy check result was written to GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:06:20,751] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:20,751] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:20,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94aedeed-032f-4a41-a247-835671f3f0a8/dqc_reference/checkm_data
[2024-01-24 14:06:20,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:20,832] [INFO] Task started: CheckM
[2024-01-24 14:06:20,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/checkm_input GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:08:34,573] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:34,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:34,597] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:34,597] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:34,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:08:34,598] [INFO] Task started: Blastn
[2024-01-24 14:08:34,598] [INFO] Running command: blastn -query GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg94aedeed-032f-4a41-a247-835671f3f0a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:35,852] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:35,855] [INFO] Selected 8 target genomes.
[2024-01-24 14:08:35,855] [INFO] Target genome list was writen to GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:35,863] [INFO] Task started: fastANI
[2024-01-24 14:08:35,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg6daf27dd-63f1-4eec-8afb-8621468b346f/GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna.gz --refList GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:58,671] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:58,679] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:58,679] [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_900109545.1	s__Stigmatella aurantiaca	100.0	3087	3090	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.281	N/A	N/A	N/A	N/A	1	conclusive
GCF_900111745.1	s__Stigmatella erecta	95.2734	2751	3090	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	88.149	2427	3090	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Stigmatella	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016926755.1	s__Hyalangium sp016926755	83.2524	1548	3090	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Hyalangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737315.1	s__Hyalangium minutum	82.2555	1835	3090	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Hyalangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002305875.1	s__Cystobacter fuscus_A	81.0022	1628	3090	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Cystobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000335475.2	s__Cystobacter fuscus	80.9341	1617	3090	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Cystobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010894405.1	s__Myxococcus caerfyrddinensis	80.8828	1617	3090	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:58,681] [INFO] GTDB search result was written to GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:58,681] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:58,685] [INFO] DFAST_QC result json was written to GCF_900109545.1_IMG-taxon_2693429895_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:08:58,685] [INFO] DFAST_QC completed!
[2024-01-24 14:08:58,685] [INFO] Total running time: 0h3m59s