[2024-01-24 15:03:30,013] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:30,015] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:30,015] [INFO] DQC Reference Directory: /var/lib/cwl/stgddfaeb3e-5068-4fa6-a996-5fa4b9a1504f/dqc_reference
[2024-01-24 15:03:31,427] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:31,428] [INFO] Task started: Prodigal
[2024-01-24 15:03:31,428] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f0a2b9d-fd36-47b8-946d-fb49539c88ac/GCF_025995515.1_ASM2599551v1_genomic.fna.gz | prodigal -d GCF_025995515.1_ASM2599551v1_genomic.fna/cds.fna -a GCF_025995515.1_ASM2599551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:39,363] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:39,364] [INFO] Task started: HMMsearch
[2024-01-24 15:03:39,364] [INFO] Running command: hmmsearch --tblout GCF_025995515.1_ASM2599551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddfaeb3e-5068-4fa6-a996-5fa4b9a1504f/dqc_reference/reference_markers.hmm GCF_025995515.1_ASM2599551v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:39,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:39,602] [INFO] Found 6/6 markers.
[2024-01-24 15:03:39,628] [INFO] Query marker FASTA was written to GCF_025995515.1_ASM2599551v1_genomic.fna/markers.fasta
[2024-01-24 15:03:39,629] [INFO] Task started: Blastn
[2024-01-24 15:03:39,629] [INFO] Running command: blastn -query GCF_025995515.1_ASM2599551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddfaeb3e-5068-4fa6-a996-5fa4b9a1504f/dqc_reference/reference_markers.fasta -out GCF_025995515.1_ASM2599551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:40,478] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:40,482] [INFO] Selected 18 target genomes.
[2024-01-24 15:03:40,483] [INFO] Target genome list was writen to GCF_025995515.1_ASM2599551v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:40,490] [INFO] Task started: fastANI
[2024-01-24 15:03:40,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f0a2b9d-fd36-47b8-946d-fb49539c88ac/GCF_025995515.1_ASM2599551v1_genomic.fna.gz --refList GCF_025995515.1_ASM2599551v1_genomic.fna/target_genomes.txt --output GCF_025995515.1_ASM2599551v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:54,243] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:54,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddfaeb3e-5068-4fa6-a996-5fa4b9a1504f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:54,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddfaeb3e-5068-4fa6-a996-5fa4b9a1504f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:54,258] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:54,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:54,258] [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 peroxydans	strain=LMG 1635	GCA_011516745.1	104098	104098	type	True	99.9956	803	803	95	conclusive
Acetobacter peroxydans	strain=NBRC 13755	GCA_006539345.1	104098	104098	type	True	99.9941	794	803	95	conclusive
Acetobacter papayae	strain=JCM 25143	GCA_000613285.1	1076592	1076592	type	True	86.2763	620	803	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	79.7971	415	803	95	below_threshold
Acetobacter fabarum	strain=LMG 24244	GCA_011516925.1	483199	483199	type	True	79.4595	350	803	95	below_threshold
Acetobacter lovaniensis	strain=LMG 1617	GCA_011516875.1	104100	104100	type	True	79.4554	350	803	95	below_threshold
Acetobacter lovaniensis	strain=DSM 4491	GCA_014207635.1	104100	104100	type	True	79.4383	352	803	95	below_threshold
Acetobacter okinawensis	strain=JCM 25146	GCA_000613865.1	1076594	1076594	type	True	79.1614	315	803	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848	GCA_011516865.1	431306	431306	type	True	79.037	310	803	95	below_threshold
Acetobacter senegalensis	strain=LMG 23690	GCA_001580995.1	446692	446692	type	True	78.5762	219	803	95	below_threshold
Komagataeibacter sucrofermentans	strain=LMG 18788	GCA_003207865.1	1053551	1053551	type	True	77.8783	197	803	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.0367	103	803	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	77.0117	103	803	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.2133	78	803	95	below_threshold
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	75.9293	68	803	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	75.9225	56	803	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	75.9176	67	803	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:54,260] [INFO] DFAST Taxonomy check result was written to GCF_025995515.1_ASM2599551v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:54,260] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:54,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:54,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddfaeb3e-5068-4fa6-a996-5fa4b9a1504f/dqc_reference/checkm_data
[2024-01-24 15:03:54,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:54,289] [INFO] Task started: CheckM
[2024-01-24 15:03:54,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025995515.1_ASM2599551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025995515.1_ASM2599551v1_genomic.fna/checkm_input GCF_025995515.1_ASM2599551v1_genomic.fna/checkm_result
[2024-01-24 15:04:23,114] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:23,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:23,134] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:23,134] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:23,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025995515.1_ASM2599551v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:23,135] [INFO] Task started: Blastn
[2024-01-24 15:04:23,136] [INFO] Running command: blastn -query GCF_025995515.1_ASM2599551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddfaeb3e-5068-4fa6-a996-5fa4b9a1504f/dqc_reference/reference_markers_gtdb.fasta -out GCF_025995515.1_ASM2599551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:24,557] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:24,560] [INFO] Selected 15 target genomes.
[2024-01-24 15:04:24,560] [INFO] Target genome list was writen to GCF_025995515.1_ASM2599551v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:24,570] [INFO] Task started: fastANI
[2024-01-24 15:04:24,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f0a2b9d-fd36-47b8-946d-fb49539c88ac/GCF_025995515.1_ASM2599551v1_genomic.fna.gz --refList GCF_025995515.1_ASM2599551v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025995515.1_ASM2599551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:34,274] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:34,287] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:34,287] [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_006539345.1	s__Acetobacter peroxydans	99.9941	794	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_000613285.1	s__Acetobacter papayae	86.2694	621	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017377745.1	s__Acetobacter suratthaniensis	85.6864	657	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017377735.1	s__Acetobacter sp017377735	79.7894	416	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516925.1	s__Acetobacter fabarum	79.4595	350	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.96	97.82	0.89	0.87	4	-
GCF_014207635.1	s__Acetobacter lovaniensis	79.4383	352	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008365315.1	s__Acetobacter sp008365315	79.3935	354	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613865.1	s__Acetobacter okinawensis	79.1715	315	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.60	97.58	0.84	0.82	3	-
GCF_002153655.1	s__Acetobacter okinawensis_A	79.0568	292	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499675.1	s__Acetobacter ghanensis	78.9839	310	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011516935.1	s__Acetobacter farinalis	78.7289	274	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580995.1	s__Acetobacter senegalensis	78.5762	219	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.25	96.97	0.85	0.80	6	-
GCF_003207865.1	s__Komagataeibacter sucrofermentans	77.862	198	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343615.1	s__Paracraurococcus sp004343615	76.0847	56	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622225.1	s__Roseomonas mucosa	75.9388	66	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.41	98.67	0.95	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:34,289] [INFO] GTDB search result was written to GCF_025995515.1_ASM2599551v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:34,289] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:34,293] [INFO] DFAST_QC result json was written to GCF_025995515.1_ASM2599551v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:34,293] [INFO] DFAST_QC completed!
[2024-01-24 15:04:34,294] [INFO] Total running time: 0h1m4s