[2024-01-24 12:14:33,741] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,742] [INFO] DQC Reference Directory: /var/lib/cwl/stgae8dee2a-c3f3-436a-8aaa-17e77aadd11c/dqc_reference
[2024-01-24 12:14:35,166] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,167] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,167] [INFO] Running command: gunzip -c /var/lib/cwl/stg86735e7b-980c-443f-93c8-7ee538859b5d/GCF_012933655.1_ASM1293365v1_genomic.fna.gz | prodigal -d GCF_012933655.1_ASM1293365v1_genomic.fna/cds.fna -a GCF_012933655.1_ASM1293365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:22,767] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:22,768] [INFO] Task started: HMMsearch
[2024-01-24 12:16:22,768] [INFO] Running command: hmmsearch --tblout GCF_012933655.1_ASM1293365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae8dee2a-c3f3-436a-8aaa-17e77aadd11c/dqc_reference/reference_markers.hmm GCF_012933655.1_ASM1293365v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:23,173] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:23,174] [INFO] Found 6/6 markers.
[2024-01-24 12:16:23,268] [INFO] Query marker FASTA was written to GCF_012933655.1_ASM1293365v1_genomic.fna/markers.fasta
[2024-01-24 12:16:23,268] [INFO] Task started: Blastn
[2024-01-24 12:16:23,268] [INFO] Running command: blastn -query GCF_012933655.1_ASM1293365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae8dee2a-c3f3-436a-8aaa-17e77aadd11c/dqc_reference/reference_markers.fasta -out GCF_012933655.1_ASM1293365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:23,959] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:23,971] [INFO] Selected 16 target genomes.
[2024-01-24 12:16:23,971] [INFO] Target genome list was writen to GCF_012933655.1_ASM1293365v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:23,988] [INFO] Task started: fastANI
[2024-01-24 12:16:23,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg86735e7b-980c-443f-93c8-7ee538859b5d/GCF_012933655.1_ASM1293365v1_genomic.fna.gz --refList GCF_012933655.1_ASM1293365v1_genomic.fna/target_genomes.txt --output GCF_012933655.1_ASM1293365v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:17:03,657] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:03,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae8dee2a-c3f3-436a-8aaa-17e77aadd11c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:17:03,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae8dee2a-c3f3-436a-8aaa-17e77aadd11c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:17:03,667] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:17:03,667] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:17:03,668] [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
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	100.0	4082	4121	95	conclusive
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	87.4803	2858	4121	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	87.2428	2915	4121	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	84.7496	1774	4121	95	below_threshold
Myxococcus virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	84.4341	2005	4121	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	84.3428	2032	4121	95	below_threshold
Myxococcus xanthus	strain=DSM 16526	GCA_900106535.1	34	34	type	True	84.1828	2037	4121	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	83.4758	2159	4121	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	82.2924	1983	4121	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	82.2185	1806	4121	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.0217	621	4121	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.0164	606	4121	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	74.904	485	4121	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	74.885	108	4121	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	74.8809	109	4121	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	74.879	110	4121	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:17:03,669] [INFO] DFAST Taxonomy check result was written to GCF_012933655.1_ASM1293365v1_genomic.fna/tc_result.tsv
[2024-01-24 12:17:03,669] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:17:03,669] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:17:03,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae8dee2a-c3f3-436a-8aaa-17e77aadd11c/dqc_reference/checkm_data
[2024-01-24 12:17:03,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:17:03,784] [INFO] Task started: CheckM
[2024-01-24 12:17:03,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012933655.1_ASM1293365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012933655.1_ASM1293365v1_genomic.fna/checkm_input GCF_012933655.1_ASM1293365v1_genomic.fna/checkm_result
[2024-01-24 12:24:20,749] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:20,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:20,782] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:20,782] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:20,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012933655.1_ASM1293365v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:20,783] [INFO] Task started: Blastn
[2024-01-24 12:24:20,783] [INFO] Running command: blastn -query GCF_012933655.1_ASM1293365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae8dee2a-c3f3-436a-8aaa-17e77aadd11c/dqc_reference/reference_markers_gtdb.fasta -out GCF_012933655.1_ASM1293365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:22,235] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:22,238] [INFO] Selected 12 target genomes.
[2024-01-24 12:24:22,238] [INFO] Target genome list was writen to GCF_012933655.1_ASM1293365v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:22,246] [INFO] Task started: fastANI
[2024-01-24 12:24:22,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg86735e7b-980c-443f-93c8-7ee538859b5d/GCF_012933655.1_ASM1293365v1_genomic.fna.gz --refList GCF_012933655.1_ASM1293365v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012933655.1_ASM1293365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:03,809] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:03,817] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:03,817] [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_012933655.1	s__Myxococcus fallax	100.0	4082	4121	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010894435.1	s__Myxococcus trucidator	87.4628	2865	4121	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	87.2864	2905	4121	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	86.6372	2856	4121	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002305895.1	s__Myxococcus macrosporus	84.6989	2107	4121	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.54	98.54	0.93	0.93	2	-
GCF_006402735.1	s__Myxococcus xanthus_A	84.4045	2064	4121	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.2302	99.44	99.22	0.98	0.96	5	-
GCF_900101905.1	s__Myxococcus virescens	84.3338	2035	4121	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.8216	98.11	97.12	0.95	0.93	4	-
GCF_000280925.3	s__Myxococcus hansupus	83.9861	2055	4121	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111765.1	s__Myxococcus fulvus	83.6271	2259	4121	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.03	95.70	0.96	0.91	4	-
GCF_010894455.1	s__Myxococcus eversor	83.61	2233	4121	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	99.18	99.18	0.94	0.94	2	-
GCF_013336725.1	s__Myxococcus sp013336725	83.5304	2277	4121	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.23	98.12	0.95	0.94	5	-
GCF_017301635.1	s__Myxococcus sp017301635	82.9313	2074	4121	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 12:25:03,818] [INFO] GTDB search result was written to GCF_012933655.1_ASM1293365v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:03,819] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:03,821] [INFO] DFAST_QC result json was written to GCF_012933655.1_ASM1293365v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:03,822] [INFO] DFAST_QC completed!
[2024-01-24 12:25:03,822] [INFO] Total running time: 0h10m30s