[2024-01-25 19:09:05,535] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:05,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:05,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg49a4b440-ebf8-4ac4-adbe-79f7be413170/dqc_reference
[2024-01-25 19:09:06,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:06,687] [INFO] Task started: Prodigal
[2024-01-25 19:09:06,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg164b4e30-a9e0-4055-931a-49713a4186f7/GCF_003387095.1_ASM338709v1_genomic.fna.gz | prodigal -d GCF_003387095.1_ASM338709v1_genomic.fna/cds.fna -a GCF_003387095.1_ASM338709v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:06,358] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:06,359] [INFO] Task started: HMMsearch
[2024-01-25 19:10:06,359] [INFO] Running command: hmmsearch --tblout GCF_003387095.1_ASM338709v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49a4b440-ebf8-4ac4-adbe-79f7be413170/dqc_reference/reference_markers.hmm GCF_003387095.1_ASM338709v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:06,819] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:06,821] [INFO] Found 6/6 markers.
[2024-01-25 19:10:06,913] [INFO] Query marker FASTA was written to GCF_003387095.1_ASM338709v1_genomic.fna/markers.fasta
[2024-01-25 19:10:06,913] [INFO] Task started: Blastn
[2024-01-25 19:10:06,913] [INFO] Running command: blastn -query GCF_003387095.1_ASM338709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49a4b440-ebf8-4ac4-adbe-79f7be413170/dqc_reference/reference_markers.fasta -out GCF_003387095.1_ASM338709v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:07,628] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:07,631] [INFO] Selected 23 target genomes.
[2024-01-25 19:10:07,632] [INFO] Target genome list was writen to GCF_003387095.1_ASM338709v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:07,655] [INFO] Task started: fastANI
[2024-01-25 19:10:07,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg164b4e30-a9e0-4055-931a-49713a4186f7/GCF_003387095.1_ASM338709v1_genomic.fna.gz --refList GCF_003387095.1_ASM338709v1_genomic.fna/target_genomes.txt --output GCF_003387095.1_ASM338709v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:53,276] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:53,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49a4b440-ebf8-4ac4-adbe-79f7be413170/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:53,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49a4b440-ebf8-4ac4-adbe-79f7be413170/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:53,290] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:10:53,290] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:10:53,291] [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
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	100.0	4113	4117	95	conclusive
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	99.9884	4114	4117	95	conclusive
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	92.3096	3087	4117	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	80.691	1859	4117	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	80.6873	1574	4117	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	80.6448	1594	4117	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	80.529	1915	4117	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	80.2469	1481	4117	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	80.0796	1594	4117	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	80.015	1474	4117	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	79.9118	1612	4117	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	79.8962	1637	4117	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	79.725	1501	4117	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_001399755.1	381306	381306	type	True	75.1449	148	4117	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_900101365.1	381306	381306	type	True	75.1031	155	4117	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	75.101	478	4117	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	74.983	187	4117	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	74.9132	334	4117	95	below_threshold
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	74.899	223	4117	95	below_threshold
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	74.8795	204	4117	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	74.875	200	4117	95	below_threshold
Micromonospora inaquosa	strain=LB39	GCA_003857055.1	2203716	2203716	type	True	74.871	251	4117	95	below_threshold
Nesterenkonia halophila	strain=DSM 16378	GCA_009467795.1	302044	302044	type	True	74.842	119	4117	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:53,292] [INFO] DFAST Taxonomy check result was written to GCF_003387095.1_ASM338709v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:53,292] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:53,293] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:53,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49a4b440-ebf8-4ac4-adbe-79f7be413170/dqc_reference/checkm_data
[2024-01-25 19:10:53,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:53,401] [INFO] Task started: CheckM
[2024-01-25 19:10:53,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003387095.1_ASM338709v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003387095.1_ASM338709v1_genomic.fna/checkm_input GCF_003387095.1_ASM338709v1_genomic.fna/checkm_result
[2024-01-25 19:17:02,999] [INFO] Task succeeded: CheckM
[2024-01-25 19:17:03,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:17:03,029] [INFO] ===== Completeness check finished =====
[2024-01-25 19:17:03,029] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:17:03,030] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003387095.1_ASM338709v1_genomic.fna/markers.fasta)
[2024-01-25 19:17:03,030] [INFO] Task started: Blastn
[2024-01-25 19:17:03,030] [INFO] Running command: blastn -query GCF_003387095.1_ASM338709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49a4b440-ebf8-4ac4-adbe-79f7be413170/dqc_reference/reference_markers_gtdb.fasta -out GCF_003387095.1_ASM338709v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:17:04,230] [INFO] Task succeeded: Blastn
[2024-01-25 19:17:04,233] [INFO] Selected 6 target genomes.
[2024-01-25 19:17:04,233] [INFO] Target genome list was writen to GCF_003387095.1_ASM338709v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:17:04,276] [INFO] Task started: fastANI
[2024-01-25 19:17:04,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg164b4e30-a9e0-4055-931a-49713a4186f7/GCF_003387095.1_ASM338709v1_genomic.fna.gz --refList GCF_003387095.1_ASM338709v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003387095.1_ASM338709v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:17:28,857] [INFO] Task succeeded: fastANI
[2024-01-25 19:17:28,862] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:17:28,863] [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_001027285.1	s__Archangium gephyra	99.9884	4114	4117	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000733295.1	s__Archangium violaceum	92.3108	3088	4117	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	95.60	95.60	0.86	0.86	2	-
GCF_016859125.1	s__Archangium violaceum_A	86.7527	2588	4117	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003044305.1	s__Archangium sp003044305	86.2877	2773	4117	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016887565.1	s__Archangium violaceum_B	86.1982	2775	4117	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Archangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000335475.2	s__Cystobacter fuscus	83.7389	2259	4117	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Cystobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:17:28,864] [INFO] GTDB search result was written to GCF_003387095.1_ASM338709v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:17:28,865] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:17:28,899] [INFO] DFAST_QC result json was written to GCF_003387095.1_ASM338709v1_genomic.fna/dqc_result.json
[2024-01-25 19:17:28,899] [INFO] DFAST_QC completed!
[2024-01-25 19:17:28,899] [INFO] Total running time: 0h8m23s