[2024-01-24 13:17:15,747] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:15,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:15,751] [INFO] DQC Reference Directory: /var/lib/cwl/stg276550d0-5cb6-4471-aeea-3d4ded916c71/dqc_reference
[2024-01-24 13:17:17,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:17,158] [INFO] Task started: Prodigal
[2024-01-24 13:17:17,158] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fec6a22-b4ea-4075-b3a3-2687f3dfbb0f/GCF_024170465.1_ASM2417046v1_genomic.fna.gz | prodigal -d GCF_024170465.1_ASM2417046v1_genomic.fna/cds.fna -a GCF_024170465.1_ASM2417046v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:26,551] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:26,551] [INFO] Task started: HMMsearch
[2024-01-24 13:17:26,551] [INFO] Running command: hmmsearch --tblout GCF_024170465.1_ASM2417046v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg276550d0-5cb6-4471-aeea-3d4ded916c71/dqc_reference/reference_markers.hmm GCF_024170465.1_ASM2417046v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:26,820] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:26,821] [INFO] Found 6/6 markers.
[2024-01-24 13:17:26,847] [INFO] Query marker FASTA was written to GCF_024170465.1_ASM2417046v1_genomic.fna/markers.fasta
[2024-01-24 13:17:26,848] [INFO] Task started: Blastn
[2024-01-24 13:17:26,848] [INFO] Running command: blastn -query GCF_024170465.1_ASM2417046v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg276550d0-5cb6-4471-aeea-3d4ded916c71/dqc_reference/reference_markers.fasta -out GCF_024170465.1_ASM2417046v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:27,669] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:27,672] [INFO] Selected 25 target genomes.
[2024-01-24 13:17:27,673] [INFO] Target genome list was writen to GCF_024170465.1_ASM2417046v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:27,682] [INFO] Task started: fastANI
[2024-01-24 13:17:27,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fec6a22-b4ea-4075-b3a3-2687f3dfbb0f/GCF_024170465.1_ASM2417046v1_genomic.fna.gz --refList GCF_024170465.1_ASM2417046v1_genomic.fna/target_genomes.txt --output GCF_024170465.1_ASM2417046v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:43,356] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:43,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg276550d0-5cb6-4471-aeea-3d4ded916c71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:43,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg276550d0-5cb6-4471-aeea-3d4ded916c71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:43,370] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:43,370] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:43,370] [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
Natronospira proteinivora	strain=BSker1	GCA_024170465.1	1807133	1807133	type	True	100.0	974	974	95	conclusive
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.9443	104	974	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	76.8938	68	974	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	76.785	66	974	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	76.6012	79	974	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	76.414	74	974	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.3487	64	974	95	below_threshold
Ectothiorhodospira marina	strain=DSM 241	GCA_900109495.1	1396821	1396821	type	True	76.2981	84	974	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.2585	90	974	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.2171	72	974	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.1059	85	974	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	76.0102	74	974	95	below_threshold
Pseudomonas nitroreducens	strain=DSM 14399	GCA_012986245.1	46680	46680	suspected-type	True	75.9077	59	974	95	below_threshold
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	75.8866	57	974	95	below_threshold
Xanthomonas cucurbitae	strain=CFBP2542	GCA_002939885.1	56453	56453	type	True	75.6946	50	974	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	75.4562	57	974	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:43,371] [INFO] DFAST Taxonomy check result was written to GCF_024170465.1_ASM2417046v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:43,372] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:43,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:43,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg276550d0-5cb6-4471-aeea-3d4ded916c71/dqc_reference/checkm_data
[2024-01-24 13:17:43,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:43,403] [INFO] Task started: CheckM
[2024-01-24 13:17:43,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024170465.1_ASM2417046v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024170465.1_ASM2417046v1_genomic.fna/checkm_input GCF_024170465.1_ASM2417046v1_genomic.fna/checkm_result
[2024-01-24 13:18:15,638] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:15,639] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:15,658] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:15,659] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:15,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024170465.1_ASM2417046v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:15,660] [INFO] Task started: Blastn
[2024-01-24 13:18:15,660] [INFO] Running command: blastn -query GCF_024170465.1_ASM2417046v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg276550d0-5cb6-4471-aeea-3d4ded916c71/dqc_reference/reference_markers_gtdb.fasta -out GCF_024170465.1_ASM2417046v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:16,948] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:16,952] [INFO] Selected 25 target genomes.
[2024-01-24 13:18:16,952] [INFO] Target genome list was writen to GCF_024170465.1_ASM2417046v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:16,987] [INFO] Task started: fastANI
[2024-01-24 13:18:16,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fec6a22-b4ea-4075-b3a3-2687f3dfbb0f/GCF_024170465.1_ASM2417046v1_genomic.fna.gz --refList GCF_024170465.1_ASM2417046v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024170465.1_ASM2417046v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:29,539] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:29,550] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:18:29,550] [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_003558125.1	s__SLPV01 sp003558125	79.0556	405	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SLND01;f__SLND01;g__SLPV01	95.0	99.79	99.79	0.87	0.87	2	-
GCA_007131825.1	s__SLPV01 sp007131825	78.539	208	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SLND01;f__SLND01;g__SLPV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	76.943	104	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584115.1	s__Ectothiorhodospira mobilis	76.7449	99	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623495.1	s__JAAZVP01 sp018623495	76.6321	75	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378965.1	s__Thioalkalivibrio_A thiocyanodenitrificans	76.6012	79	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009295635.1	s__S0819 sp009295635	76.4903	96	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__S0819	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002840095.1	s__Sulfurivermis sp002840095	76.3384	88	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009497875.2	s__JADGBD01 sp009497875	76.2612	68	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__JADGBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751635.1	s__Inmirania thermothiophila	76.1971	73	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	76.0886	86	974	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	-
GCF_002091755.1	s__Pseudomonas nitroreducens	75.8866	57	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	98.47	95.19	0.93	0.83	16	-
GCF_002939885.1	s__Xanthomonas cucurbitae	75.6946	50	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	99.30	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:29,552] [INFO] GTDB search result was written to GCF_024170465.1_ASM2417046v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:29,553] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:29,556] [INFO] DFAST_QC result json was written to GCF_024170465.1_ASM2417046v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:29,556] [INFO] DFAST_QC completed!
[2024-01-24 13:18:29,557] [INFO] Total running time: 0h1m14s