[2023-06-28 12:03:35,400] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:03:35,402] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:03:35,402] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ab57af2-5ad7-4601-b374-3bacc0cd0b9f/dqc_reference
[2023-06-28 12:03:36,503] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:03:36,504] [INFO] Task started: Prodigal
[2023-06-28 12:03:36,504] [INFO] Running command: gunzip -c /var/lib/cwl/stgf344b020-f41c-45bc-9858-89ee5942de7f/GCA_019310105.1_ASM1931010v1_genomic.fna.gz | prodigal -d GCA_019310105.1_ASM1931010v1_genomic.fna/cds.fna -a GCA_019310105.1_ASM1931010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:03:51,009] [INFO] Task succeeded: Prodigal
[2023-06-28 12:03:51,009] [INFO] Task started: HMMsearch
[2023-06-28 12:03:51,009] [INFO] Running command: hmmsearch --tblout GCA_019310105.1_ASM1931010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ab57af2-5ad7-4601-b374-3bacc0cd0b9f/dqc_reference/reference_markers.hmm GCA_019310105.1_ASM1931010v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:03:51,268] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:03:51,269] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf344b020-f41c-45bc-9858-89ee5942de7f/GCA_019310105.1_ASM1931010v1_genomic.fna.gz]
[2023-06-28 12:03:51,317] [INFO] Query marker FASTA was written to GCA_019310105.1_ASM1931010v1_genomic.fna/markers.fasta
[2023-06-28 12:03:51,317] [INFO] Task started: Blastn
[2023-06-28 12:03:51,318] [INFO] Running command: blastn -query GCA_019310105.1_ASM1931010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ab57af2-5ad7-4601-b374-3bacc0cd0b9f/dqc_reference/reference_markers.fasta -out GCA_019310105.1_ASM1931010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:03:51,924] [INFO] Task succeeded: Blastn
[2023-06-28 12:03:51,927] [INFO] Selected 30 target genomes.
[2023-06-28 12:03:51,928] [INFO] Target genome list was writen to GCA_019310105.1_ASM1931010v1_genomic.fna/target_genomes.txt
[2023-06-28 12:03:51,932] [INFO] Task started: fastANI
[2023-06-28 12:03:51,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgf344b020-f41c-45bc-9858-89ee5942de7f/GCA_019310105.1_ASM1931010v1_genomic.fna.gz --refList GCA_019310105.1_ASM1931010v1_genomic.fna/target_genomes.txt --output GCA_019310105.1_ASM1931010v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:04:22,268] [INFO] Task succeeded: fastANI
[2023-06-28 12:04:22,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ab57af2-5ad7-4601-b374-3bacc0cd0b9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:04:22,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ab57af2-5ad7-4601-b374-3bacc0cd0b9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:04:22,281] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:04:22,281] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:04:22,282] [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
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1992	81	1318	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	75.0643	98	1318	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.0594	52	1318	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.0546	52	1318	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	75.014	103	1318	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	75.0135	103	1318	95	below_threshold
Nocardioides stalactiti	strain=1.0914	GCA_014180715.1	2755356	2755356	type	True	74.9901	52	1318	95	below_threshold
Myxococcus xanthus	strain=DSM 16526	GCA_900106535.1	34	34	type	True	74.9544	70	1318	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	74.9277	73	1318	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	74.9167	111	1318	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	74.9104	99	1318	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	74.8781	79	1318	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.8548	105	1318	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.8275	81	1318	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.8232	82	1318	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	74.7501	81	1318	95	below_threshold
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	74.5736	55	1318	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:04:22,283] [INFO] DFAST Taxonomy check result was written to GCA_019310105.1_ASM1931010v1_genomic.fna/tc_result.tsv
[2023-06-28 12:04:22,284] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:04:22,284] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:04:22,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ab57af2-5ad7-4601-b374-3bacc0cd0b9f/dqc_reference/checkm_data
[2023-06-28 12:04:22,285] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:04:22,344] [INFO] Task started: CheckM
[2023-06-28 12:04:22,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310105.1_ASM1931010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310105.1_ASM1931010v1_genomic.fna/checkm_input GCA_019310105.1_ASM1931010v1_genomic.fna/checkm_result
[2023-06-28 12:05:04,670] [INFO] Task succeeded: CheckM
[2023-06-28 12:05:04,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:05:04,690] [INFO] ===== Completeness check finished =====
[2023-06-28 12:05:04,690] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:05:04,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310105.1_ASM1931010v1_genomic.fna/markers.fasta)
[2023-06-28 12:05:04,691] [INFO] Task started: Blastn
[2023-06-28 12:05:04,691] [INFO] Running command: blastn -query GCA_019310105.1_ASM1931010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ab57af2-5ad7-4601-b374-3bacc0cd0b9f/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310105.1_ASM1931010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:05:05,618] [INFO] Task succeeded: Blastn
[2023-06-28 12:05:05,621] [INFO] Selected 26 target genomes.
[2023-06-28 12:05:05,621] [INFO] Target genome list was writen to GCA_019310105.1_ASM1931010v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:05:05,632] [INFO] Task started: fastANI
[2023-06-28 12:05:05,632] [INFO] Running command: fastANI --query /var/lib/cwl/stgf344b020-f41c-45bc-9858-89ee5942de7f/GCA_019310105.1_ASM1931010v1_genomic.fna.gz --refList GCA_019310105.1_ASM1931010v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310105.1_ASM1931010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:05:25,614] [INFO] Task succeeded: fastANI
[2023-06-28 12:05:25,623] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:05:25,624] [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
GCA_006226595.1	s__M1803 sp006226595	76.0062	168	1318	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__M1803	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938035.1	s__JAFGVK01 sp016938035	75.838	147	1318	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__JAFGVK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875315.1	s__SXON01 sp016875315	75.8055	98	1318	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015489145.1	s__S143-5 sp015489145	75.6673	129	1318	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__S143-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875435.1	s__SXON01 sp016875435	75.5923	93	1318	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717595.1	s__JADKFE01 sp016717595	75.5701	99	1318	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__CAJQPC01;g__JADKFE01	95.0	98.32	98.16	0.91	0.88	3	-
GCA_003694325.1	s__J125 sp003694325	75.5124	112	1318	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__J125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693595.1	s__REDI01 sp007693595	75.4762	76	1318	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__REDI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897935.1	s__CAIUDO01 sp903897935	75.4746	120	1318	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__CAIUDO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861005.1	s__CAIOSP01 sp903861005	75.4718	92	1318	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__CAIOSP01	95.0	99.96	99.95	0.97	0.97	4	-
GCA_002862545.1	s__GCA-2862545 sp002862545	75.3988	102	1318	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__GCA-2862545	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992495.1	s__Reyranella soli	75.0594	52	1318	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	75.0546	52	1318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000720535.1	s__Streptomyces halstedii	74.7103	76	1318	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.49	96.54	0.92	0.83	17	-
GCF_014650495.1	s__Streptomyces cinnamoneus	74.6475	78	1318	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:05:25,625] [INFO] GTDB search result was written to GCA_019310105.1_ASM1931010v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:05:25,626] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:05:25,632] [INFO] DFAST_QC result json was written to GCA_019310105.1_ASM1931010v1_genomic.fna/dqc_result.json
[2023-06-28 12:05:25,632] [INFO] DFAST_QC completed!
[2023-06-28 12:05:25,632] [INFO] Total running time: 0h1m50s