[2024-01-25 17:39:06,261] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:06,262] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:06,263] [INFO] DQC Reference Directory: /var/lib/cwl/stga0f830a2-5e96-4075-8435-91ed3dc9650b/dqc_reference
[2024-01-25 17:39:07,377] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:07,379] [INFO] Task started: Prodigal
[2024-01-25 17:39:07,379] [INFO] Running command: gunzip -c /var/lib/cwl/stg149a90da-a83f-4d7a-bda6-0f8106a58c73/GCF_001263175.1_ASM126317v1_genomic.fna.gz | prodigal -d GCF_001263175.1_ASM126317v1_genomic.fna/cds.fna -a GCF_001263175.1_ASM126317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:17,607] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:17,607] [INFO] Task started: HMMsearch
[2024-01-25 17:39:17,607] [INFO] Running command: hmmsearch --tblout GCF_001263175.1_ASM126317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0f830a2-5e96-4075-8435-91ed3dc9650b/dqc_reference/reference_markers.hmm GCF_001263175.1_ASM126317v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:17,870] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:17,871] [INFO] Found 6/6 markers.
[2024-01-25 17:39:17,908] [INFO] Query marker FASTA was written to GCF_001263175.1_ASM126317v1_genomic.fna/markers.fasta
[2024-01-25 17:39:17,908] [INFO] Task started: Blastn
[2024-01-25 17:39:17,908] [INFO] Running command: blastn -query GCF_001263175.1_ASM126317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0f830a2-5e96-4075-8435-91ed3dc9650b/dqc_reference/reference_markers.fasta -out GCF_001263175.1_ASM126317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:18,654] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:18,657] [INFO] Selected 22 target genomes.
[2024-01-25 17:39:18,657] [INFO] Target genome list was writen to GCF_001263175.1_ASM126317v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:18,674] [INFO] Task started: fastANI
[2024-01-25 17:39:18,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg149a90da-a83f-4d7a-bda6-0f8106a58c73/GCF_001263175.1_ASM126317v1_genomic.fna.gz --refList GCF_001263175.1_ASM126317v1_genomic.fna/target_genomes.txt --output GCF_001263175.1_ASM126317v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:46,294] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:46,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0f830a2-5e96-4075-8435-91ed3dc9650b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:46,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0f830a2-5e96-4075-8435-91ed3dc9650b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:46,308] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:39:46,308] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:39:46,308] [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
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	100.0	1448	1450	95	conclusive
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	76.6372	320	1450	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	76.5973	293	1450	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	76.5022	216	1450	95	below_threshold
Corallococcus exercitus	strain=AB043A	GCA_003611585.1	2316736	2316736	type	True	76.4459	242	1450	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	76.4398	294	1450	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	76.3872	285	1450	95	below_threshold
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	76.3066	244	1450	95	below_threshold
Corallococcus interemptor	strain=AB047A	GCA_003668875.1	2316720	2316720	type	True	76.2874	258	1450	95	below_threshold
Corallococcus aberystwythensis	strain=AB050A	GCA_003612165.1	2316722	2316722	type	True	76.2574	255	1450	95	below_threshold
Corallococcus exiguus	strain=DSM 14696	GCA_009909105.1	83462	83462	type	True	76.2518	253	1450	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	76.2	241	1450	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	76.1336	282	1450	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	76.1265	306	1450	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.5928	134	1450	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	75.5457	133	1450	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	75.5063	122	1450	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	75.4507	121	1450	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	75.193	137	1450	95	below_threshold
Deinococcus pimensis	strain=DSM 21231	GCA_000519345.1	309888	309888	type	True	75.0219	95	1450	95	below_threshold
Deinococcus apachensis	strain=DSM 19763	GCA_000381345.1	309886	309886	type	True	74.9734	50	1450	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	74.9325	120	1450	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:46,309] [INFO] DFAST Taxonomy check result was written to GCF_001263175.1_ASM126317v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:46,310] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:46,310] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:46,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0f830a2-5e96-4075-8435-91ed3dc9650b/dqc_reference/checkm_data
[2024-01-25 17:39:46,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:46,352] [INFO] Task started: CheckM
[2024-01-25 17:39:46,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001263175.1_ASM126317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001263175.1_ASM126317v1_genomic.fna/checkm_input GCF_001263175.1_ASM126317v1_genomic.fna/checkm_result
[2024-01-25 17:40:19,800] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:19,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:19,835] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:19,835] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:19,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001263175.1_ASM126317v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:19,836] [INFO] Task started: Blastn
[2024-01-25 17:40:19,836] [INFO] Running command: blastn -query GCF_001263175.1_ASM126317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0f830a2-5e96-4075-8435-91ed3dc9650b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001263175.1_ASM126317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:21,277] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:21,281] [INFO] Selected 24 target genomes.
[2024-01-25 17:40:21,282] [INFO] Target genome list was writen to GCF_001263175.1_ASM126317v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:21,322] [INFO] Task started: fastANI
[2024-01-25 17:40:21,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg149a90da-a83f-4d7a-bda6-0f8106a58c73/GCF_001263175.1_ASM126317v1_genomic.fna.gz --refList GCF_001263175.1_ASM126317v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001263175.1_ASM126317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:43,117] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:43,130] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:43,131] [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_001263175.1	s__Vulgatibacter incomptus	100.0	1448	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Vulgatibacteraceae;g__Vulgatibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003242475.1	s__ZC4RG40 sp003242475	78.0498	325	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Vulgatibacteraceae;g__ZC4RG40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214955.1	s__JACRMN01 sp016214955	76.8819	268	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JACRMN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964525.1	s__Anaeromyxobacter sp000964525	76.7846	277	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013385.1	s__Anaeromyxobacter dehalogenans_B	76.7211	319	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022145.1	s__Anaeromyxobacter dehalogenans	76.7067	315	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	97.16	97.16	0.92	0.92	2	-
GCF_003600865.1	s__Corallococcus sp003600865	76.6042	228	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	99.50	99.50	0.97	0.97	2	-
GCA_016458225.1	s__Corallococcus sp016458225	76.5777	233	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013340205.1	s__R267 sp013340205	76.5521	324	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__R267	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001768075.1	s__R267 sp001768075	76.5397	211	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__R267	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903874275.1	s__CAIOAK01 sp903874275	76.5201	219	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__CAIOAK01	95.0	99.83	99.81	0.95	0.94	3	-
GCF_000017505.1	s__Anaeromyxobacter sp000017505	76.5126	315	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023645.1	s__Geomonas sp000023645	76.4958	75	1450	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888115.1	s__40CM-4-68-19 sp005888115	76.4536	155	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__40CM-4-68-19;g__40CM-4-68-19	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733295.1	s__Archangium violaceum	76.4532	290	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	95.60	95.60	0.86	0.86	2	-
GCA_016793095.1	s__JAEUJQ01 sp016793095	75.8991	260	1450	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__JAEUJQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240325.1	s__Rubrivivax sp018240325	75.3211	98	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218805.1	s__JACRCW01 sp016218805	75.2367	71	1450	d__Bacteria;p__Myxococcota;c__JACRCW01;o__JACRCW01;f__JACRCW01;g__JACRCW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364605.1	s__Nocardioides sp000364605	75.132	82	1450	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805655.1	s__CADCTF01 sp902805655	75.0655	60	1450	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCTF01;g__CADCTF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919045.1	s__CAILLO01 sp903919045	74.9651	81	1450	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__UBA5734;g__CAILLO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813345.1	s__JACCRW01 sp013813345	74.8347	53	1450	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACCRW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:43,132] [INFO] GTDB search result was written to GCF_001263175.1_ASM126317v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:43,133] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:43,137] [INFO] DFAST_QC result json was written to GCF_001263175.1_ASM126317v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:43,137] [INFO] DFAST_QC completed!
[2024-01-25 17:40:43,137] [INFO] Total running time: 0h1m37s