[2024-01-24 13:57:57,146] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:57,149] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:57,149] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f7ef809-ab74-4e75-9582-ebfd557a146b/dqc_reference
[2024-01-24 13:57:58,403] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:58,404] [INFO] Task started: Prodigal
[2024-01-24 13:57:58,404] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b83f264-ab32-4cf2-9666-b92b915409a9/GCF_014174215.1_ASM1417421v1_genomic.fna.gz | prodigal -d GCF_014174215.1_ASM1417421v1_genomic.fna/cds.fna -a GCF_014174215.1_ASM1417421v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:11,629] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:11,629] [INFO] Task started: HMMsearch
[2024-01-24 13:58:11,630] [INFO] Running command: hmmsearch --tblout GCF_014174215.1_ASM1417421v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f7ef809-ab74-4e75-9582-ebfd557a146b/dqc_reference/reference_markers.hmm GCF_014174215.1_ASM1417421v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:11,973] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:11,975] [INFO] Found 6/6 markers.
[2024-01-24 13:58:12,011] [INFO] Query marker FASTA was written to GCF_014174215.1_ASM1417421v1_genomic.fna/markers.fasta
[2024-01-24 13:58:12,012] [INFO] Task started: Blastn
[2024-01-24 13:58:12,012] [INFO] Running command: blastn -query GCF_014174215.1_ASM1417421v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f7ef809-ab74-4e75-9582-ebfd557a146b/dqc_reference/reference_markers.fasta -out GCF_014174215.1_ASM1417421v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:12,933] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:12,937] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:12,937] [INFO] Target genome list was writen to GCF_014174215.1_ASM1417421v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:12,964] [INFO] Task started: fastANI
[2024-01-24 13:58:12,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b83f264-ab32-4cf2-9666-b92b915409a9/GCF_014174215.1_ASM1417421v1_genomic.fna.gz --refList GCF_014174215.1_ASM1417421v1_genomic.fna/target_genomes.txt --output GCF_014174215.1_ASM1417421v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:24,347] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:24,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f7ef809-ab74-4e75-9582-ebfd557a146b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:24,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f7ef809-ab74-4e75-9582-ebfd557a146b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:24,359] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:24,359] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:24,359] [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
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	88.5418	984	1392	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	88.358	974	1392	95	below_threshold
Gluconacetobacter liquefaciens	strain=DSM 5603	GCA_003350405.1	89584	89584	type	True	88.3336	966	1392	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	88.2993	956	1392	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	83.6582	769	1392	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	83.6213	755	1392	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	83.578	771	1392	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.4195	291	1392	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	77.0076	232	1392	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.8232	215	1392	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.6788	206	1392	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.0942	184	1392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:24,361] [INFO] DFAST Taxonomy check result was written to GCF_014174215.1_ASM1417421v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:24,361] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:24,361] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:24,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f7ef809-ab74-4e75-9582-ebfd557a146b/dqc_reference/checkm_data
[2024-01-24 13:58:24,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:24,405] [INFO] Task started: CheckM
[2024-01-24 13:58:24,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014174215.1_ASM1417421v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014174215.1_ASM1417421v1_genomic.fna/checkm_input GCF_014174215.1_ASM1417421v1_genomic.fna/checkm_result
[2024-01-24 13:59:07,441] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:07,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:07,466] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:07,466] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:07,466] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014174215.1_ASM1417421v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:07,467] [INFO] Task started: Blastn
[2024-01-24 13:59:07,467] [INFO] Running command: blastn -query GCF_014174215.1_ASM1417421v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f7ef809-ab74-4e75-9582-ebfd557a146b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014174215.1_ASM1417421v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:08,998] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:09,001] [INFO] Selected 6 target genomes.
[2024-01-24 13:59:09,001] [INFO] Target genome list was writen to GCF_014174215.1_ASM1417421v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:09,002] [INFO] Task started: fastANI
[2024-01-24 13:59:09,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b83f264-ab32-4cf2-9666-b92b915409a9/GCF_014174215.1_ASM1417421v1_genomic.fna.gz --refList GCF_014174215.1_ASM1417421v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014174215.1_ASM1417421v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:15,972] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:15,983] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:59:15,983] [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_014174215.1	s__Gluconacetobacter tumulicola	100.0	1385	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	inconclusive
GCF_014174395.1	s__Gluconacetobacter aggeris	96.1128	1166	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_014174375.1	s__Gluconacetobacter asukensis	96.0469	1156	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.0437	N/A	N/A	N/A	N/A	1	inconclusive
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	89.4751	991	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174165.1	s__Gluconacetobacter dulcium	88.5561	983	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	98.93	97.86	0.94	0.88	3	-
GCF_003350405.1	s__Gluconacetobacter liquefaciens	88.327	966	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:15,985] [INFO] GTDB search result was written to GCF_014174215.1_ASM1417421v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:15,986] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:15,990] [INFO] DFAST_QC result json was written to GCF_014174215.1_ASM1417421v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:15,991] [INFO] DFAST_QC completed!
[2024-01-24 13:59:15,991] [INFO] Total running time: 0h1m19s