[2024-01-24 13:58:42,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:42,167] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:42,167] [INFO] DQC Reference Directory: /var/lib/cwl/stg19fe7405-f35f-4f67-94e6-8192bc097cb9/dqc_reference
[2024-01-24 13:58:43,482] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:43,483] [INFO] Task started: Prodigal
[2024-01-24 13:58:43,483] [INFO] Running command: gunzip -c /var/lib/cwl/stg05970eea-acb0-4db9-919f-a03055879fc1/GCF_017377715.1_ASM1737771v1_genomic.fna.gz | prodigal -d GCF_017377715.1_ASM1737771v1_genomic.fna/cds.fna -a GCF_017377715.1_ASM1737771v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:56,493] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:56,493] [INFO] Task started: HMMsearch
[2024-01-24 13:58:56,493] [INFO] Running command: hmmsearch --tblout GCF_017377715.1_ASM1737771v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19fe7405-f35f-4f67-94e6-8192bc097cb9/dqc_reference/reference_markers.hmm GCF_017377715.1_ASM1737771v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:56,780] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:56,782] [INFO] Found 6/6 markers.
[2024-01-24 13:58:56,832] [INFO] Query marker FASTA was written to GCF_017377715.1_ASM1737771v1_genomic.fna/markers.fasta
[2024-01-24 13:58:56,832] [INFO] Task started: Blastn
[2024-01-24 13:58:56,832] [INFO] Running command: blastn -query GCF_017377715.1_ASM1737771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19fe7405-f35f-4f67-94e6-8192bc097cb9/dqc_reference/reference_markers.fasta -out GCF_017377715.1_ASM1737771v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:57,673] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:57,677] [INFO] Selected 19 target genomes.
[2024-01-24 13:58:57,678] [INFO] Target genome list was writen to GCF_017377715.1_ASM1737771v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:57,686] [INFO] Task started: fastANI
[2024-01-24 13:58:57,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg05970eea-acb0-4db9-919f-a03055879fc1/GCF_017377715.1_ASM1737771v1_genomic.fna.gz --refList GCF_017377715.1_ASM1737771v1_genomic.fna/target_genomes.txt --output GCF_017377715.1_ASM1737771v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:11,023] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:11,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19fe7405-f35f-4f67-94e6-8192bc097cb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:11,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19fe7405-f35f-4f67-94e6-8192bc097cb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:11,038] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:11,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:11,038] [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
Acetobacter sacchari	strain=TBRC 11175	GCA_017377715.1	2661687	2661687	type	True	100.0	1478	1480	95	conclusive
Acetobacter nitrogenifigens	strain=NBRC 105050	GCA_007991375.1	285268	285268	type	True	92.7931	1189	1480	95	below_threshold
Acetobacter nitrogenifigens	strain=DSM 23921	GCA_000429165.1	285268	285268	type	True	92.7773	1212	1480	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	79.5683	292	1480	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	79.5184	294	1480	95	below_threshold
Acetobacter aceti	strain=NBRC 14818	GCA_000193495.2	435	435	type	True	78.7353	252	1480	95	below_threshold
Acetobacter aceti	strain=DSM 3508	GCA_004341595.1	435	435	type	True	78.6859	256	1480	95	below_threshold
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	78.4831	267	1480	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	78.2725	260	1480	95	below_threshold
Acetobacter fallax	strain=LMG 1636	GCA_011516735.1	1737473	1737473	type	True	78.2418	228	1480	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	78.2035	260	1480	95	below_threshold
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	77.7149	191	1480	95	below_threshold
Komagataeibacter nataicola	strain=LMG 1536	GCA_003207795.1	265960	265960	type	True	77.6138	203	1480	95	below_threshold
Komagataeibacter melaceti	strain=AV382	GCA_003403295.1	2766577	2766577	type	True	77.5306	189	1480	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.9009	146	1480	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.6522	114	1480	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.6464	105	1480	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.3894	101	1480	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	75.6672	68	1480	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:11,040] [INFO] DFAST Taxonomy check result was written to GCF_017377715.1_ASM1737771v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:11,041] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:11,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:11,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19fe7405-f35f-4f67-94e6-8192bc097cb9/dqc_reference/checkm_data
[2024-01-24 13:59:11,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:11,085] [INFO] Task started: CheckM
[2024-01-24 13:59:11,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017377715.1_ASM1737771v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017377715.1_ASM1737771v1_genomic.fna/checkm_input GCF_017377715.1_ASM1737771v1_genomic.fna/checkm_result
[2024-01-24 13:59:50,729] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:50,731] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:50,753] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:50,754] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:50,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017377715.1_ASM1737771v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:50,755] [INFO] Task started: Blastn
[2024-01-24 13:59:50,755] [INFO] Running command: blastn -query GCF_017377715.1_ASM1737771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19fe7405-f35f-4f67-94e6-8192bc097cb9/dqc_reference/reference_markers_gtdb.fasta -out GCF_017377715.1_ASM1737771v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:51,862] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:51,866] [INFO] Selected 18 target genomes.
[2024-01-24 13:59:51,866] [INFO] Target genome list was writen to GCF_017377715.1_ASM1737771v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:51,888] [INFO] Task started: fastANI
[2024-01-24 13:59:51,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg05970eea-acb0-4db9-919f-a03055879fc1/GCF_017377715.1_ASM1737771v1_genomic.fna.gz --refList GCF_017377715.1_ASM1737771v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017377715.1_ASM1737771v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:05,218] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:05,232] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:05,233] [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_017377715.1	s__Acetobacter sacchari	100.0	1478	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002153745.1	s__Acetobacter sp002153745	94.8573	830	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429165.1	s__Acetobacter nitrogenifigens	92.7922	1211	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	79.4873	295	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_011516765.1	s__Acetobacter sicerae	78.5341	267	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174165.1	s__Gluconacetobacter dulcium	78.4831	267	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	98.93	97.86	0.94	0.88	3	-
GCF_011516735.1	s__Acetobacter fallax	78.2263	229	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011516755.1	s__Acetobacter conturbans	78.2139	257	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350405.1	s__Gluconacetobacter liquefaciens	78.1694	264	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	78.1616	259	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174305.1	s__Gluconacetobacter johannae	78.0947	249	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019083805.1	s__Acetobacter estunensis_A	78.0543	239	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174215.1	s__Gluconacetobacter tumulicola	78.0503	262	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCA_002409645.1	s__Acetobacter sp002409645	77.793	219	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004302915.1	s__Komagataeibacter xylinus_C	77.72	201	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571345.1	s__Komagataeibacter xylinus	77.7178	187	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.56	99.15	0.93	0.88	3	-
GCF_003403295.1	s__Komagataeibacter melaceti	77.5146	190	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970625.1	s__CAJCJG01 sp903970625	76.4305	107	1480	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAJCJG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:05,235] [INFO] GTDB search result was written to GCF_017377715.1_ASM1737771v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:05,236] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:05,240] [INFO] DFAST_QC result json was written to GCF_017377715.1_ASM1737771v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:05,240] [INFO] DFAST_QC completed!
[2024-01-24 14:00:05,240] [INFO] Total running time: 0h1m23s