[2024-01-25 18:47:20,444] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:47:20,446] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:47:20,446] [INFO] DQC Reference Directory: /var/lib/cwl/stg814828f4-6fb0-4b0e-b304-129d21db866c/dqc_reference
[2024-01-25 18:47:21,608] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:47:21,609] [INFO] Task started: Prodigal
[2024-01-25 18:47:21,609] [INFO] Running command: gunzip -c /var/lib/cwl/stg89a74469-64f0-4b49-83ad-a22418eec4fa/GCF_014202975.1_ASM1420297v1_genomic.fna.gz | prodigal -d GCF_014202975.1_ASM1420297v1_genomic.fna/cds.fna -a GCF_014202975.1_ASM1420297v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:47:38,419] [INFO] Task succeeded: Prodigal
[2024-01-25 18:47:38,420] [INFO] Task started: HMMsearch
[2024-01-25 18:47:38,420] [INFO] Running command: hmmsearch --tblout GCF_014202975.1_ASM1420297v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg814828f4-6fb0-4b0e-b304-129d21db866c/dqc_reference/reference_markers.hmm GCF_014202975.1_ASM1420297v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:47:38,730] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:47:38,731] [INFO] Found 6/6 markers.
[2024-01-25 18:47:38,779] [INFO] Query marker FASTA was written to GCF_014202975.1_ASM1420297v1_genomic.fna/markers.fasta
[2024-01-25 18:47:38,780] [INFO] Task started: Blastn
[2024-01-25 18:47:38,780] [INFO] Running command: blastn -query GCF_014202975.1_ASM1420297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg814828f4-6fb0-4b0e-b304-129d21db866c/dqc_reference/reference_markers.fasta -out GCF_014202975.1_ASM1420297v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:39,602] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:39,605] [INFO] Selected 20 target genomes.
[2024-01-25 18:47:39,605] [INFO] Target genome list was writen to GCF_014202975.1_ASM1420297v1_genomic.fna/target_genomes.txt
[2024-01-25 18:47:39,630] [INFO] Task started: fastANI
[2024-01-25 18:47:39,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg89a74469-64f0-4b49-83ad-a22418eec4fa/GCF_014202975.1_ASM1420297v1_genomic.fna.gz --refList GCF_014202975.1_ASM1420297v1_genomic.fna/target_genomes.txt --output GCF_014202975.1_ASM1420297v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:59,108] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:59,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg814828f4-6fb0-4b0e-b304-129d21db866c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:59,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg814828f4-6fb0-4b0e-b304-129d21db866c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:59,123] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:47:59,123] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:59,123] [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
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	100.0	2101	2101	95	conclusive
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	78.4891	587	2101	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	78.3554	524	2101	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	78.2966	498	2101	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	78.2887	515	2101	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	78.2695	593	2101	95	below_threshold
Steroidobacter denitrificans	strain=DSM 18526	GCA_001579945.1	465721	465721	type	True	77.2352	232	2101	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	76.686	53	2101	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	76.3939	177	2101	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	76.2616	159	2101	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	76.1951	144	2101	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.0461	99	2101	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.0198	121	2101	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	75.9864	113	2101	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	75.8649	107	2101	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	75.8391	149	2101	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	75.839	139	2101	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	75.8334	106	2101	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	75.8022	62	2101	95	below_threshold
Pseudomonas baetica	strain=a390	GCA_003031005.1	674054	674054	type	True	75.7877	61	2101	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:59,125] [INFO] DFAST Taxonomy check result was written to GCF_014202975.1_ASM1420297v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:59,125] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:59,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:59,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg814828f4-6fb0-4b0e-b304-129d21db866c/dqc_reference/checkm_data
[2024-01-25 18:47:59,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:59,185] [INFO] Task started: CheckM
[2024-01-25 18:47:59,185] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202975.1_ASM1420297v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202975.1_ASM1420297v1_genomic.fna/checkm_input GCF_014202975.1_ASM1420297v1_genomic.fna/checkm_result
[2024-01-25 18:48:52,044] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:52,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:52,063] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:52,063] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:52,064] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202975.1_ASM1420297v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:52,064] [INFO] Task started: Blastn
[2024-01-25 18:48:52,064] [INFO] Running command: blastn -query GCF_014202975.1_ASM1420297v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg814828f4-6fb0-4b0e-b304-129d21db866c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202975.1_ASM1420297v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:53,645] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:53,648] [INFO] Selected 17 target genomes.
[2024-01-25 18:48:53,648] [INFO] Target genome list was writen to GCF_014202975.1_ASM1420297v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:53,675] [INFO] Task started: fastANI
[2024-01-25 18:48:53,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg89a74469-64f0-4b49-83ad-a22418eec4fa/GCF_014202975.1_ASM1420297v1_genomic.fna.gz --refList GCF_014202975.1_ASM1420297v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202975.1_ASM1420297v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:49:10,834] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:10,845] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:49:10,845] [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_014202975.1	s__Povalibacter uvarum	100.0	2101	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Povalibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009932555.1	s__Steroidobacter_A agaridevorans	78.5093	584	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	99.33	99.33	0.96	0.96	2	-
GCF_004138485.1	s__Steroidobacter_A soli	78.3481	525	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801985.1	s__Steroidobacter_A sp016801985	78.3006	500	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138335.1	s__Steroidobacter_A agariperforans	78.2759	592	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242495.1	s__ZC4RG39 sp003242495	77.9086	256	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG39	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790065.1	s__Steroidobacter_A sp016790065	77.8753	396	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898785.1	s__CAIUGU01 sp903898785	77.6948	209	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIUGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884105.1	s__CAIUGU01 sp903884105	77.5445	214	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIUGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577615.1	s__JAAYXG01 sp017577615	77.5025	264	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__JAAYXG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012516015.1	s__JAAYXG01 sp012516015	77.3567	214	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__JAAYXG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001579945.1	s__Steroidobacter denitrificans	77.2412	233	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241455.1	s__FEN-1191 sp018241455	76.9217	119	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__FEN-1191	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240295.1	s__Plasticicumulans sp003962905	76.3665	151	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCA_002995625.1	s__UDEA-SF1 sp002995625	76.3027	108	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__UDEA-SF1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813455.1	s__Pseudomonas_E baetica	75.8242	61	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.98	95.55	0.93	0.86	4	-
GCA_009782025.1	s__Azonexus sp009782025	75.4878	51	2101	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:49:10,847] [INFO] GTDB search result was written to GCF_014202975.1_ASM1420297v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:49:10,848] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:49:10,851] [INFO] DFAST_QC result json was written to GCF_014202975.1_ASM1420297v1_genomic.fna/dqc_result.json
[2024-01-25 18:49:10,851] [INFO] DFAST_QC completed!
[2024-01-25 18:49:10,852] [INFO] Total running time: 0h1m50s