[2024-01-24 13:50:26,391] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:26,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:26,393] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fcf970f-3695-48d4-8bcb-c94bdceca94c/dqc_reference
[2024-01-24 13:50:28,441] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:28,442] [INFO] Task started: Prodigal
[2024-01-24 13:50:28,442] [INFO] Running command: gunzip -c /var/lib/cwl/stg476f679c-e4d6-4d92-b465-a4cebadd2219/GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/cds.fna -a GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:51:07,325] [INFO] Task succeeded: Prodigal
[2024-01-24 13:51:07,325] [INFO] Task started: HMMsearch
[2024-01-24 13:51:07,326] [INFO] Running command: hmmsearch --tblout GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fcf970f-3695-48d4-8bcb-c94bdceca94c/dqc_reference/reference_markers.hmm GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:51:07,765] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:51:07,766] [INFO] Found 6/6 markers.
[2024-01-24 13:51:07,857] [INFO] Query marker FASTA was written to GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:51:07,857] [INFO] Task started: Blastn
[2024-01-24 13:51:07,858] [INFO] Running command: blastn -query GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fcf970f-3695-48d4-8bcb-c94bdceca94c/dqc_reference/reference_markers.fasta -out GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:08,620] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:08,624] [INFO] Selected 15 target genomes.
[2024-01-24 13:51:08,624] [INFO] Target genome list was writen to GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:51:08,631] [INFO] Task started: fastANI
[2024-01-24 13:51:08,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg476f679c-e4d6-4d92-b465-a4cebadd2219/GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna.gz --refList GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:42,941] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:42,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fcf970f-3695-48d4-8bcb-c94bdceca94c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:42,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fcf970f-3695-48d4-8bcb-c94bdceca94c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:42,961] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:51:42,961] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:51:42,961] [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
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	100.0	3581	3583	95	conclusive
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	99.9806	3519	3583	95	conclusive
Myxococcus eversor	strain=AB053B	GCA_010894455.1	2709661	2709661	type	True	87.0713	2836	3583	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	86.9833	2715	3583	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	86.0935	2528	3583	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	83.7392	2417	3583	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	83.5859	1767	3583	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	82.27	1908	3583	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	82.1441	1895	3583	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.2288	513	3583	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	75.043	115	3583	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	75.0318	380	3583	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	75.0313	203	3583	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	74.8598	327	3583	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	74.8192	422	3583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:51:42,963] [INFO] DFAST Taxonomy check result was written to GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:51:42,964] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:42,964] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:42,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fcf970f-3695-48d4-8bcb-c94bdceca94c/dqc_reference/checkm_data
[2024-01-24 13:51:42,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:43,058] [INFO] Task started: CheckM
[2024-01-24 13:51:43,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/checkm_input GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:56:37,340] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:37,346] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:37,376] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:37,377] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:37,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:56:37,379] [INFO] Task started: Blastn
[2024-01-24 13:56:37,379] [INFO] Running command: blastn -query GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fcf970f-3695-48d4-8bcb-c94bdceca94c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:38,760] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:38,765] [INFO] Selected 9 target genomes.
[2024-01-24 13:56:38,766] [INFO] Target genome list was writen to GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:38,777] [INFO] Task started: fastANI
[2024-01-24 13:56:38,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg476f679c-e4d6-4d92-b465-a4cebadd2219/GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna.gz --refList GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:08,509] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:08,520] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:08,520] [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_900111765.1	s__Myxococcus fulvus	100.0	3581	3583	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.03	95.70	0.96	0.91	4	conclusive
GCF_013336725.1	s__Myxococcus sp013336725	87.085	2880	3583	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.23	98.12	0.95	0.94	5	-
GCF_010894455.1	s__Myxococcus eversor	87.0727	2835	3583	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	99.18	99.18	0.94	0.94	2	-
GCF_000331735.1	s__Myxococcus stipitatus	86.1	2526	3583	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301635.1	s__Myxococcus sp017301635	85.9389	2549	3583	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933655.1	s__Myxococcus fallax	83.7866	2218	3583	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010894405.1	s__Myxococcus caerfyrddinensis	83.7843	2404	3583	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301735.1	s__Myxococcus sp017301735	83.6303	2387	3583	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656495.1	s__Myxococcus sp014656495	83.4362	2071	3583	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:08,522] [INFO] GTDB search result was written to GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:08,522] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:08,526] [INFO] DFAST_QC result json was written to GCF_900111765.1_IMG-taxon_2693429886_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:57:08,556] [INFO] DFAST_QC completed!
[2024-01-24 13:57:08,559] [INFO] Total running time: 0h6m42s